PDB-2r7q: Crystal Structure of VP1 apoenzyme of Rotavirus SA11 (C-terminal ...

ID or keywords:

Entry

Database: PDB / ID: 2r7q

Title

Crystal Structure of VP1 apoenzyme of Rotavirus SA11 (C-terminal hexahistidine-tagged)

Components

RNA-dependent RNA polymerase

Keywords

TRANSFERASE / Viral protein / RNA-dependent RNA polymerase / single subunit polymerase fold / fingers / palm / thumb / right hand configuration / RNA-directed RNA polymerase

Function / homology

Function and homology information

viral genome replication / virion component / RNA-directed RNA polymerase / RNA-dependent RNA polymerase activity / nucleotide binding / DNA-templated transcription / RNA binding
Similarity search - Function

Biological species

Simian rotavirus

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MIRAS /

MAD / Resolution: 2.9 Å

Authors

Lu, X. / Harrison, S.C. / Tao, Y.J. / Patton, J.T. / Nibert, M.L.

Citation

Journal: Structure / Year: 2008
Title: Mechanism for coordinated RNA packaging and genome replication by rotavirus polymerase VP1.
Authors: Lu, X. / McDonald, S.M. / Tortorici, M.A. / Tao, Y.J. / Vasquez-Del Carpio, R. / Nibert, M.L. / Patton, J.T. / Harrison, S.C.

History

Deposition	Sep 9, 2007	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jul 29, 2008	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Version format compliance
Revision 1.2	Oct 25, 2017	Group: Refinement description / Category: software Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.3	Feb 21, 2024	Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	2r7q.cif.gz	228.7 KB	Display	PDBx/mmCIF format
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Validation report

Summary document	2r7q_validation.pdf.gz	420.9 KB	Display	wwPDB validaton report
Full document	2r7q_full_validation.pdf.gz	452.8 KB	Display
Data in XML	2r7q_validation.xml.gz	40.1 KB	Display
Data in CIF	2r7q_validation.cif.gz	53.6 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/r7/2r7q ftp://data.pdbj.org/pub/pdb/validation_reports/r7/2r7q	HTTPS FTP

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Related structure data

Related structure data	2r7oC 2r7rC 2r7sC 2r7tC 2r7uC 2r7vC 2r7wC 2r7xC C: citing same article (ref.)
Similar structure data	2r7x-1 2r7x-2 2r7u-d 2r7w-d 2r7t-d 2r7o-d 2r7s-d 2r7v-d 2r7r-d 5k2m-2 Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: RNA-dependent RNA polymerase

126 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author

Unit cell

Length a, b, c (Å)	76.384, 112.474, 143.051
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein	RNA-dependent RNA polymerase Mass: 126324.453 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Simian rotavirus / Strain: SA11 / Gene: gene 1 / Plasmid: pCRBac / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): sf21 / References: UniProt: O37061

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 2.45 Å³/Da / Density % sol: 49.76 %
Crystal grow	Temperature: 285 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 1 microliter of VP1 at 10 mg/ml in 25 mM Na-HEPES, pH 7.8, 100 mM NaCl mixed with 2 microliter of crystallization buffer [25 mM Na-MES, pH 6.5, 1.5% (w/v) PEG 3350] and allowing the drop to ...Details: 1 microliter of VP1 at 10 mg/ml in 25 mM Na-HEPES, pH 7.8, 100 mM NaCl mixed with 2 microliter of crystallization buffer [25 mM Na-MES, pH 6.5, 1.5% (w/v) PEG 3350] and allowing the drop to equilibrate at 12 C by hanging-drop vapor diffusion with a well solution identical in composition to the drop except for the protein. With micro-seeding, thin, plate-like crystals appeared after 1 day and grew to full size in about two weeks, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 285K

Crystal

Density Matthews: 2.45 Å³/Da / Density % sol: 49.76 %

Crystal grow

Temperature: 285 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 1 microliter of VP1 at 10 mg/ml in 25 mM Na-HEPES, pH 7.8, 100 mM NaCl mixed with 2 microliter of crystallization buffer [25 mM Na-MES, pH 6.5, 1.5% (w/v) PEG 3350] and allowing the drop to ...

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Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

ALS

/ Beamline: 8.2.1 / Wavelength: 1.1808 Å

Detector

Type: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 10, 2004 / Details: Superbend (5.0 T, single pole)

Radiation

Monochromator: Double crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 1.1808 Å / Relative weight: 1

Reflection

Redundancy: 3.9 % / Av σ(I) over netI: 15.7 / Number: 108692 / R_merge(I) obs: 0.055 / Χ²: 1.04 / D res high: 2.9 Å / D res low: 30 Å / Num. obs: 28000 / % possible obs: 99.8

Diffraction reflection shell

Highest resolution (Å)	Lowest resolution (Å)	% possible obs (%)	ID	R_merge(I) obs	Chi squared	Redundancy
6.23	30	99.5	1	0.022	1.03	3.7
4.95	6.23	99.9	1	0.038	1.083	3.9
4.33	4.95	99.9	1	0.031	1.089	4
3.93	4.33	100	1	0.041	1.008	4
3.65	3.93	100	1	0.065	1.018	4
3.44	3.65	99.8	1	0.092	1.06	4
3.27	3.44	99.7	1	0.137	1.062	3.9
3.12	3.27	99.9	1	0.208	0.992	3.8
3	3.12	99.8	1	0.319	1.04	3.8
2.9	3	99.1	1	0.426	1.035	3.7

Reflection

Resolution: 2.9→30 Å / Num. obs: 28000 / % possible obs: 99.8 % / Redundancy: 3.9 % / R_merge(I) obs: 0.055 / Χ²: 1.042 / Net I/σ(I): 15.7

Reflection shell

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Num. unique all	Χ²	% possible all
2.9-3	3.7	0.426	2693	1.035	99.1
3-3.12	3.8	0.319	2774	1.04	99.8
3.12-3.27	3.8	0.208	2759	0.992	99.9
3.27-3.44	3.9	0.137	2765	1.062	99.7
3.44-3.65	4	0.092	2790	1.06	99.8
3.65-3.93	4	0.065	2750	1.018	100
3.93-4.33	4	0.041	2820	1.008	100
4.33-4.95	4	0.031	2819	1.089	99.9
4.95-6.23	3.9	0.038	2857	1.083	99.9
6.23-30	3.7	0.022	2973	1.03	99.5

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Phasing

Phasing

Method:

MAD

Phasing MAD

D res high: 2.9 Å / D res low: 47.33 Å / FOM acentric: 0.284 / FOM centric: 0.202 / Reflection acentric: 24408 / Reflection centric: 2968

Phasing MAD set

ID	Highest resolution (Å)	Lowest resolution (Å)	Power acentric	Power centric	Reflection acentric	Reflection centric
ISO_1	2.9	47.33	0	0	16761	2059
ISO_2	2.9	47.33	0.309	0.29	13346	1743
ISO_3	2.9	47.33	0	0	14033	1746
ISO_4	2.9	47.33	0.344	0.334	13565	1708
ISO_5	2.9	47.33	0.261	0.237	11087	1473
ISO_6	2.9	47.33	0	0	11500	843
ISO_7	2.9	47.33	0.238	0.213	12088	884
ISO_8	2.9	47.33	0.248	0.224	11412	844
ISO_9	2.9	47.33	0.884	0.815	16487	1043
ANO_1	2.9	47.33	1.153	0	16239	0
ANO_2	2.9	47.33	0.504	0	13207	0
ANO_3	2.9	47.33	0.734	0	14363	0
ANO_4	2.9	47.33	0.412	0	13910	0
ANO_5	2.9	47.33	0.44	0	11156	0
ANO_6	2.9	47.33	0.577	0	10911	0
ANO_7	2.9	47.33	0.319	0	11741	0
ANO_8	2.9	47.33	0.364	0	10815	0
ANO_9	2.9	47.33	0	0	0	0

Phasing MAD set shell

ID	Resolution (Å)	Power acentric	Power centric	Reflection acentric	Reflection centric
ISO_1	12.53-47.33	0	0	236	126
ISO_1	9.02-12.53	0	0	449	129
ISO_1	7.41-9.02	0	0	618	135
ISO_1	6.44-7.41	0	0	729	123
ISO_1	5.77-6.44	0	0	842	148
ISO_1	5.27-5.77	0	0	944	136
ISO_1	4.88-5.27	0	0	1031	129
ISO_1	4.57-4.88	0	0	1090	127
ISO_1	4.31-4.57	0	0	1167	125
ISO_1	4.09-4.31	0	0	1219	145
ISO_1	3.9-4.09	0	0	1251	127
ISO_1	3.74-3.9	0	0	1274	120
ISO_1	3.59-3.74	0	0	1303	116
ISO_1	3.46-3.59	0	0	1308	113
ISO_1	3.35-3.46	0	0	1351	110
ISO_1	3.24-3.35	0	0	1373	110
ISO_1	3.14-3.24	0	0	576	40
ISO_1	3.06-3.14	0	0	0	0
ISO_1	2.98-3.06	0	0	0	0
ISO_1	2.9-2.98	0	0	0	0
ANO_1	12.53-47.33	7.602	0	236	0
ANO_1	9.02-12.53	6.035	0	449	0
ANO_1	7.41-9.02	5.24	0	618	0
ANO_1	6.44-7.41	3.22	0	726	0
ANO_1	5.77-6.44	2.62	0	841	0
ANO_1	5.27-5.77	2.026	0	941	0
ANO_1	4.88-5.27	1.687	0	1024	0
ANO_1	4.57-4.88	1.426	0	1077	0
ANO_1	4.31-4.57	1.133	0	1135	0
ANO_1	4.09-4.31	0.844	0	1181	0
ANO_1	3.9-4.09	0.699	0	1187	0
ANO_1	3.74-3.9	0.543	0	1208	0
ANO_1	3.59-3.74	0.453	0	1227	0
ANO_1	3.46-3.59	0.371	0	1248	0
ANO_1	3.35-3.46	0.331	0	1286	0
ANO_1	3.24-3.35	0.3	0	1312	0
ANO_1	3.14-3.24	0.303	0	543	0
ANO_1	3.06-3.14	0	0	0	0
ANO_1	2.98-3.06	0	0	0	0
ANO_1	2.9-2.98	0	0	0	0
ISO_2	12.53-47.33	0.734	0.529	228	112
ISO_2	9.02-12.53	0.67	0.481	449	127
ISO_2	7.41-9.02	0.573	0.419	618	134
ISO_2	6.44-7.41	0.501	0.361	729	122
ISO_2	5.77-6.44	0.454	0.314	842	148
ISO_2	5.27-5.77	0.372	0.249	944	136
ISO_2	4.88-5.27	0.3	0.237	1030	128
ISO_2	4.57-4.88	0.242	0.183	1087	124
ISO_2	4.31-4.57	0.214	0.164	1141	122
ISO_2	4.09-4.31	0.185	0.124	1175	134
ISO_2	3.9-4.09	0.168	0.112	1200	117
ISO_2	3.74-3.9	0.15	0.104	1206	112
ISO_2	3.59-3.74	0.137	0.088	1225	108
ISO_2	3.46-3.59	0.118	0.072	1237	98
ISO_2	3.35-3.46	0.113	0.067	235	21
ISO_2	3.24-3.35	0	0	0	0
ISO_2	3.14-3.24	0	0	0	0
ISO_2	3.06-3.14	0	0	0	0
ISO_2	2.98-3.06	0	0	0	0
ISO_2	2.9-2.98	0	0	0	0
ANO_2	12.53-47.33	5.336	0	228	0
ANO_2	9.02-12.53	3.697	0	449	0
ANO_2	7.41-9.02	2.621	0	618	0
ANO_2	6.44-7.41	1.516	0	726	0
ANO_2	5.77-6.44	1.053	0	841	0
ANO_2	5.27-5.77	0.788	0	941	0
ANO_2	4.88-5.27	0.635	0	1018	0
ANO_2	4.57-4.88	0.551	0	1071	0
ANO_2	4.31-4.57	0.402	0	1111	0
ANO_2	4.09-4.31	0.322	0	1161	0
ANO_2	3.9-4.09	0.256	0	1176	0
ANO_2	3.74-3.9	0.189	0	1194	0
ANO_2	3.59-3.74	0.161	0	1216	0
ANO_2	3.46-3.59	0.134	0	1227	0
ANO_2	3.35-3.46	0.128	0	230	0
ANO_2	3.24-3.35	0	0	0	0
ANO_2	3.14-3.24	0	0	0	0
ANO_2	3.06-3.14	0	0	0	0
ANO_2	2.98-3.06	0	0	0	0
ANO_2	2.9-2.98	0	0	0	0
ISO_3	12.53-47.33	0	0	236	126
ISO_3	9.02-12.53	0	0	447	119
ISO_3	7.41-9.02	0	0	615	119
ISO_3	6.44-7.41	0	0	725	110
ISO_3	5.77-6.44	0	0	840	136
ISO_3	5.27-5.77	0	0	943	124
ISO_3	4.88-5.27	0	0	1031	119
ISO_3	4.57-4.88	0	0	1090	123
ISO_3	4.31-4.57	0	0	1167	123
ISO_3	4.09-4.31	0	0	1216	141
ISO_3	3.9-4.09	0	0	1250	127
ISO_3	3.74-3.9	0	0	1271	119
ISO_3	3.59-3.74	0	0	1290	107
ISO_3	3.46-3.59	0	0	1283	103
ISO_3	3.35-3.46	0	0	629	50
ISO_3	3.24-3.35	0	0	0	0
ISO_3	3.14-3.24	0	0	0	0
ISO_3	3.06-3.14	0	0	0	0
ISO_3	2.98-3.06	0	0	0	0
ISO_3	2.9-2.98	0	0	0	0
ANO_3	12.53-47.33	4.504	0	236	0
ANO_3	9.02-12.53	3.83	0	447	0
ANO_3	7.41-9.02	2.951	0	615	0
ANO_3	6.44-7.41	1.775	0	725	0
ANO_3	5.77-6.44	1.24	0	836	0
ANO_3	5.27-5.77	0.991	0	940	0
ANO_3	4.88-5.27	0.842	0	1026	0
ANO_3	4.57-4.88	0.727	0	1083	0
ANO_3	4.31-4.57	0.572	0	1171	0
ANO_3	4.09-4.31	0.459	0	1239	0
ANO_3	3.9-4.09	0.389	0	1315	0
ANO_3	3.74-3.9	0.309	0	1359	0
ANO_3	3.59-3.74	0.254	0	1401	0
ANO_3	3.46-3.59	0.23	0	1353	0
ANO_3	3.35-3.46	0.213	0	617	0
ANO_3	3.24-3.35	0	0	0	0
ANO_3	3.14-3.24	0	0	0	0
ANO_3	3.06-3.14	0	0	0	0
ANO_3	2.98-3.06	0	0	0	0
ANO_3	2.9-2.98	0	0	0	0
ISO_4	12.53-47.33	1.225	0.905	236	126
ISO_4	9.02-12.53	1.044	0.756	448	119
ISO_4	7.41-9.02	0.859	0.688	615	119
ISO_4	6.44-7.41	0.717	0.501	725	110
ISO_4	5.77-6.44	0.615	0.439	839	135
ISO_4	5.27-5.77	0.469	0.358	943	124
ISO_4	4.88-5.27	0.369	0.272	1031	119
ISO_4	4.57-4.88	0.303	0.22	1090	123
ISO_4	4.31-4.57	0.265	0.19	1166	123
ISO_4	4.09-4.31	0.224	0.128	1217	141
ISO_4	3.9-4.09	0.186	0.106	1247	127
ISO_4	3.74-3.9	0.153	0.1	1270	118
ISO_4	3.59-3.74	0.129	0.084	1291	108
ISO_4	3.46-3.59	0.102	0.066	1290	101
ISO_4	3.35-3.46	0.086	0.057	157	15
ISO_4	3.24-3.35	0	0	0	0
ISO_4	3.14-3.24	0	0	0	0
ISO_4	3.06-3.14	0	0	0	0
ISO_4	2.98-3.06	0	0	0	0
ISO_4	2.9-2.98	0	0	0	0
ANO_4	12.53-47.33	3.264	0	236	0
ANO_4	9.02-12.53	2.814	0	448	0
ANO_4	7.41-9.02	1.983	0	615	0
ANO_4	6.44-7.41	1.044	0	724	0
ANO_4	5.77-6.44	0.794	0	836	0
ANO_4	5.27-5.77	0.568	0	940	0
ANO_4	4.88-5.27	0.463	0	1026	0
ANO_4	4.57-4.88	0.392	0	1080	0
ANO_4	4.31-4.57	0.32	0	1172	0
ANO_4	4.09-4.31	0.262	0	1242	0
ANO_4	3.9-4.09	0.203	0	1313	0
ANO_4	3.74-3.9	0.16	0	1368	0
ANO_4	3.59-3.74	0.142	0	1405	0
ANO_4	3.46-3.59	0.125	0	1347	0
ANO_4	3.35-3.46	0.124	0	158	0
ANO_4	3.24-3.35	0	0	0	0
ANO_4	3.14-3.24	0	0	0	0
ANO_4	3.06-3.14	0	0	0	0
ANO_4	2.98-3.06	0	0	0	0
ANO_4	2.9-2.98	0	0	0	0
ISO_5	12.53-47.33	0.576	0.421	236	126
ISO_5	9.02-12.53	0.521	0.35	447	118
ISO_5	7.41-9.02	0.468	0.323	615	119
ISO_5	6.44-7.41	0.41	0.274	725	110
ISO_5	5.77-6.44	0.378	0.274	838	136
ISO_5	5.27-5.77	0.305	0.203	943	122
ISO_5	4.88-5.27	0.242	0.193	1031	115
ISO_5	4.57-4.88	0.189	0.15	1089	122
ISO_5	4.31-4.57	0.165	0.118	1163	122
ISO_5	4.09-4.31	0.143	0.092	1216	134
ISO_5	3.9-4.09	0.13	0.072	1241	122
ISO_5	3.74-3.9	0.104	0.069	1252	104
ISO_5	3.59-3.74	0.101	0.058	291	23
ISO_5	3.46-3.59	0	0	0	0
ISO_5	3.35-3.46	0	0	0	0
ISO_5	3.24-3.35	0	0	0	0
ISO_5	3.14-3.24	0	0	0	0
ISO_5	3.06-3.14	0	0	0	0
ISO_5	2.98-3.06	0	0	0	0
ISO_5	2.9-2.98	0	0	0	0
ANO_5	12.53-47.33	3.483	0	236	0
ANO_5	9.02-12.53	2.746	0	447	0
ANO_5	7.41-9.02	1.903	0	615	0
ANO_5	6.44-7.41	1.094	0	725	0
ANO_5	5.77-6.44	0.71	0	837	0
ANO_5	5.27-5.77	0.524	0	940	0
ANO_5	4.88-5.27	0.436	0	1028	0
ANO_5	4.57-4.88	0.373	0	1079	0
ANO_5	4.31-4.57	0.276	0	1164	0
ANO_5	4.09-4.31	0.22	0	1229	0
ANO_5	3.9-4.09	0.178	0	1291	0
ANO_5	3.74-3.9	0.144	0	1269	0
ANO_5	3.59-3.74	0.138	0	296	0
ANO_5	3.46-3.59	0	0	0	0
ANO_5	3.35-3.46	0	0	0	0
ANO_5	3.24-3.35	0	0	0	0
ANO_5	3.14-3.24	0	0	0	0
ANO_5	3.06-3.14	0	0	0	0
ANO_5	2.98-3.06	0	0	0	0
ANO_5	2.9-2.98	0	0	0	0
ISO_6	12.53-47.33	0	0	181	51
ISO_6	9.02-12.53	0	0	336	50
ISO_6	7.41-9.02	0	0	469	48
ISO_6	6.44-7.41	0	0	559	53
ISO_6	5.77-6.44	0	0	662	62
ISO_6	5.27-5.77	0	0	743	58
ISO_6	4.88-5.27	0	0	817	63
ISO_6	4.57-4.88	0	0	871	58
ISO_6	4.31-4.57	0	0	944	60
ISO_6	4.09-4.31	0	0	963	65
ISO_6	3.9-4.09	0	0	971	58
ISO_6	3.74-3.9	0	0	992	57
ISO_6	3.59-3.74	0	0	1000	58
ISO_6	3.46-3.59	0	0	959	49
ISO_6	3.35-3.46	0	0	777	41
ISO_6	3.24-3.35	0	0	256	12
ISO_6	3.14-3.24	0	0	0	0
ISO_6	3.06-3.14	0	0	0	0
ISO_6	2.98-3.06	0	0	0	0
ISO_6	2.9-2.98	0	0	0	0
ANO_6	12.53-47.33	4.328	0	176	0
ANO_6	9.02-12.53	2.989	0	334	0
ANO_6	7.41-9.02	1.831	0	466	0
ANO_6	6.44-7.41	1.247	0	556	0
ANO_6	5.77-6.44	0.975	0	657	0
ANO_6	5.27-5.77	0.776	0	739	0
ANO_6	4.88-5.27	0.647	0	815	0
ANO_6	4.57-4.88	0.511	0	870	0
ANO_6	4.31-4.57	0.407	0	935	0
ANO_6	4.09-4.31	0.343	0	958	0
ANO_6	3.9-4.09	0.288	0	963	0
ANO_6	3.74-3.9	0.231	0	974	0
ANO_6	3.59-3.74	0.202	0	940	0
ANO_6	3.46-3.59	0.188	0	819	0
ANO_6	3.35-3.46	0.182	0	566	0
ANO_6	3.24-3.35	0.19	0	143	0
ANO_6	3.14-3.24	0	0	0	0
ANO_6	3.06-3.14	0	0	0	0
ANO_6	2.98-3.06	0	0	0	0
ANO_6	2.9-2.98	0	0	0	0
ISO_7	12.53-47.33	0.776	0.438	182	52
ISO_7	9.02-12.53	0.608	0.462	337	51
ISO_7	7.41-9.02	0.543	0.31	470	48
ISO_7	6.44-7.41	0.466	0.3	559	53
ISO_7	5.77-6.44	0.408	0.292	662	62
ISO_7	5.27-5.77	0.322	0.264	745	58
ISO_7	4.88-5.27	0.255	0.198	817	63
ISO_7	4.57-4.88	0.208	0.151	873	59
ISO_7	4.31-4.57	0.176	0.123	948	61
ISO_7	4.09-4.31	0.147	0.083	980	69
ISO_7	3.9-4.09	0.134	0.076	1004	60
ISO_7	3.74-3.9	0.118	0.07	1034	58
ISO_7	3.59-3.74	0.105	0.061	1054	62
ISO_7	3.46-3.59	0.094	0.057	1061	58
ISO_7	3.35-3.46	0.072	0.051	1015	57
ISO_7	3.24-3.35	0.072	0.036	347	13
ISO_7	3.14-3.24	0	0	0	0
ISO_7	3.06-3.14	0	0	0	0
ISO_7	2.98-3.06	0	0	0	0
ISO_7	2.9-2.98	0	0	0	0
ANO_7	12.53-47.33	2.219	0	177	0
ANO_7	9.02-12.53	1.51	0	335	0
ANO_7	7.41-9.02	1.11	0	468	0
ANO_7	6.44-7.41	0.717	0	555	0
ANO_7	5.77-6.44	0.533	0	657	0
ANO_7	5.27-5.77	0.462	0	741	0
ANO_7	4.88-5.27	0.374	0	816	0
ANO_7	4.57-4.88	0.307	0	873	0
ANO_7	4.31-4.57	0.241	0	952	0
ANO_7	4.09-4.31	0.185	0	992	0
ANO_7	3.9-4.09	0.161	0	1037	0
ANO_7	3.74-3.9	0.139	0	1066	0
ANO_7	3.59-3.74	0.114	0	1057	0
ANO_7	3.46-3.59	0.108	0	1016	0
ANO_7	3.35-3.46	0.104	0	788	0
ANO_7	3.24-3.35	0.11	0	211	0
ANO_7	3.14-3.24	0	0	0	0
ANO_7	3.06-3.14	0	0	0	0
ANO_7	2.98-3.06	0	0	0	0
ANO_7	2.9-2.98	0	0	0	0
ISO_8	12.53-47.33	0.785	0.438	180	51
ISO_8	9.02-12.53	0.588	0.415	335	50
ISO_8	7.41-9.02	0.517	0.316	469	49
ISO_8	6.44-7.41	0.459	0.3	558	53
ISO_8	5.77-6.44	0.394	0.332	661	62
ISO_8	5.27-5.77	0.323	0.234	743	58
ISO_8	4.88-5.27	0.248	0.222	816	63
ISO_8	4.57-4.88	0.202	0.153	868	59
ISO_8	4.31-4.57	0.18	0.129	937	58
ISO_8	4.09-4.31	0.142	0.081	957	67
ISO_8	3.9-4.09	0.136	0.081	960	58
ISO_8	3.74-3.9	0.12	0.08	980	58
ISO_8	3.59-3.74	0.109	0.059	996	54
ISO_8	3.46-3.59	0.096	0.058	950	53
ISO_8	3.35-3.46	0.079	0.055	766	40
ISO_8	3.24-3.35	0.074	0.035	236	11
ISO_8	3.14-3.24	0	0	0	0
ISO_8	3.06-3.14	0	0	0	0
ISO_8	2.98-3.06	0	0	0	0
ISO_8	2.9-2.98	0	0	0	0
ANO_8	12.53-47.33	2.191	0	177	0
ANO_8	9.02-12.53	1.788	0	333	0
ANO_8	7.41-9.02	1.245	0	468	0
ANO_8	6.44-7.41	0.826	0	557	0
ANO_8	5.77-6.44	0.592	0	655	0
ANO_8	5.27-5.77	0.452	0	740	0
ANO_8	4.88-5.27	0.395	0	815	0
ANO_8	4.57-4.88	0.338	0	864	0
ANO_8	4.31-4.57	0.259	0	928	0
ANO_8	4.09-4.31	0.213	0	944	0
ANO_8	3.9-4.09	0.174	0	946	0
ANO_8	3.74-3.9	0.151	0	960	0
ANO_8	3.59-3.74	0.126	0	938	0
ANO_8	3.46-3.59	0.122	0	810	0
ANO_8	3.35-3.46	0.115	0	544	0
ANO_8	3.24-3.35	0.151	0	136	0
ANO_8	3.14-3.24	0	0	0	0
ANO_8	3.06-3.14	0	0	0	0
ANO_8	2.98-3.06	0	0	0	0
ANO_8	2.9-2.98	0	0	0	0
ISO_9	12.53-47.33	1.845	1.389	228	56
ISO_9	9.02-12.53	1.483	0.966	449	63
ISO_9	7.41-9.02	1.372	1.026	618	72
ISO_9	6.44-7.41	1.346	1.024	728	62
ISO_9	5.77-6.44	1.228	0.807	842	77
ISO_9	5.27-5.77	1.028	0.75	943	68
ISO_9	4.88-5.27	0.805	0.739	1027	62
ISO_9	4.57-4.88	0.651	0.447	1082	66
ISO_9	4.31-4.57	0.551	0.358	1149	65
ISO_9	4.09-4.31	0.486	0.274	1205	75
ISO_9	3.9-4.09	0.44	0.243	1216	66
ISO_9	3.74-3.9	0.395	0.306	1242	63
ISO_9	3.59-3.74	0.364	0.29	1265	56
ISO_9	3.46-3.59	0.332	0.243	1282	61
ISO_9	3.35-3.46	0.305	0.252	1315	56
ISO_9	3.24-3.35	0.296	0.256	1341	49
ISO_9	3.14-3.24	0.292	0.154	555	26
ISO_9	3.06-3.14	0	0	0	0
ISO_9	2.98-3.06	0	0	0	0
ISO_9	2.9-2.98	0	0	0	0
ANO_9	12.53-47.33	0	0	0	0
ANO_9	9.02-12.53	0	0	0	0
ANO_9	7.41-9.02	0	0	0	0
ANO_9	6.44-7.41	0	0	0	0
ANO_9	5.77-6.44	0	0	0	0
ANO_9	5.27-5.77	0	0	0	0
ANO_9	4.88-5.27	0	0	0	0
ANO_9	4.57-4.88	0	0	0	0
ANO_9	4.31-4.57	0	0	0	0
ANO_9	4.09-4.31	0	0	0	0
ANO_9	3.9-4.09	0	0	0	0
ANO_9	3.74-3.9	0	0	0	0
ANO_9	3.59-3.74	0	0	0	0
ANO_9	3.46-3.59	0	0	0	0
ANO_9	3.35-3.46	0	0	0	0
ANO_9	3.24-3.35	0	0	0	0
ANO_9	3.14-3.24	0	0	0	0
ANO_9	3.06-3.14	0	0	0	0
ANO_9	2.98-3.06	0	0	0	0
ANO_9	2.9-2.98	0	0	0	0

Phasing MAD set site

ID	Cartn x (Å)	Cartn y (Å)	Cartn z (Å)	Atom type symbol	Occupancy
1	-0.11	32.442	4.826	SE-S	1.37
2	6.206	25.409	42.529	SE-S	1.08
3	9.584	20.427	45.892	SE-S	1.35
4	29.381	19.717	43.447	SE-S	1.06
5	4.71	11.735	118.885	SE-S	1.25
6	7.647	19.322	61.096	SE-S	1.6
7	30.785	26.716	138.698	SE-S	1.36
8	21.519	38.163	92.427	SE-S	1.23
9	31.278	40.933	99.357	SE-S	1.43
10	12.157	41.813	96.362	SE-S	1.07
11	23.288	51.026	85.604	SE-S	1.46
12	13.064	54.673	30.063	SE-S	1.22
13	12.55	4.571	130.193	SE-S	1.44
14	15.628	8.303	129.284	SE-S	1.12
15	16.091	43.609	81.323	SE-S	1.22
16	36.936	30.196	102.128	SE-S	1.13
17	2.578	6.926	89.608	SE-S	1.45
18	4.732	13.35	97.452	SE-S	1.25
19	3.4	35.412	8.813	SE-S	1.62
20	18.207	55.674	32.339	SE-S	1.16
21	2.48	12.681	133.431	SE-S	1.07
22	36.828	8.809	113.29	SE-S	1.18
23	30.281	18.206	133.464	SE-S	1.64
24	13.896	16.422	115.626	SE-S	1.17
25	11.792	17.049	36.294	SE-S	1.01
26	4.077	19.747	35.786	SE-S	1.04
27	31.84	2.408	38.275	SE-S	0.97
28	0.738	6.212	118.869	SE-S	1.21
29	34.101	24.649	41.747	SE-S	1.01
30	19.042	54.266	113.764	SE-S	1.03
31	28.479	0.98	40.381	SE-S	1.06

Phasing MAD shell

Resolution (Å)	FOM acentric	FOM centric	Reflection acentric	Reflection centric
12.53-47.33	0.904	0.568	236	148
9.02-12.53	0.835	0.45	449	142
7.41-9.02	0.814	0.498	618	135
6.44-7.41	0.755	0.466	730	132
5.77-6.44	0.71	0.428	842	148
5.27-5.77	0.663	0.363	944	137
4.88-5.27	0.596	0.343	1033	130
4.57-4.88	0.528	0.246	1095	128
4.31-4.57	0.466	0.196	1180	130
4.09-4.31	0.413	0.171	1251	160
3.9-4.09	0.328	0.127	1331	146
3.74-3.9	0.271	0.114	1384	148
3.59-3.74	0.217	0.097	1459	153
3.46-3.59	0.175	0.082	1524	160
3.35-3.46	0.127	0.054	1595	158
3.24-3.35	0.098	0.047	1631	162
3.14-3.24	0.031	0.01	1708	165
3.06-3.14	0	0	1762	155
2.98-3.06	0	0	1796	172
2.9-2.98	0	0	1840	159

Phasing dm

Method: Solvent flattening and Histogram matching / Reflection: 27884

Phasing dm shell

Resolution (Å)	Delta phi final	FOM	Reflection
11.55-100	45.5	0.796	505
9.03-11.55	46.5	0.881	512
7.83-9.03	44.7	0.882	528
7.01-7.83	46.9	0.87	568
6.4-7.01	44.9	0.851	645
5.93-6.4	47.9	0.866	684
5.55-5.93	49.3	0.857	738
5.23-5.55	50.3	0.877	776
4.96-5.23	48.6	0.882	835
4.73-4.96	52.1	0.893	849
4.53-4.73	53.1	0.893	894
4.36-4.53	61	0.898	937
4.2-4.36	59.8	0.884	969
4.05-4.2	63.5	0.878	992
3.93-4.05	69.1	0.872	1051
3.81-3.93	70.9	0.854	1036
3.7-3.81	71.8	0.858	1097
3.6-3.7	76.3	0.861	1119
3.51-3.6	77.6	0.852	1155
3.43-3.51	82.7	0.826	1184
3.35-3.43	84.4	0.81	1212
3.28-3.35	88.6	0.774	1225
3.21-3.28	86.8	0.744	1242
3.14-3.21	86.4	0.691	1287
3.08-3.14	90.7	0.745	1285
3.02-3.08	89.3	0.737	1356
2.97-3.02	90.8	0.713	1352
2.9-2.97	90.5	0.659	1851

-
Processing

Software

Name	Version	Classification
DENZO		data reduction
SCALEPACK		data scaling
SHARP		phasing
DM	4.2	phasing
CNS		refinement
PDB_EXTRACT	3	data extraction
ADSC	Quantum	data collection
HKL-2000		data reduction

Refinement

Method to determine structure:

MIRAS / Resolution: 2.9→30 Å / Isotropic thermal model: Isotropic / σ(F): 0

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.29	2136	7.6 %	Random 8%
R_work	0.23	-	-	-
all	0.23	27991	-	-
obs	0.23	26921	96.2 %	-

Solvent computation

B_sol: 33.215 Å²

Displacement parameters

B_iso mean: 56.908 Å²

Refinement step

Cycle: LAST / Resolution: 2.9→30 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	8686	0	0	0	8686

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target
X-RAY DIFFRACTION	c_mcbond_it	2.268	1.5
X-RAY DIFFRACTION	c_scbond_it	3.26	2
X-RAY DIFFRACTION	c_mcangle_it	3.997	2
X-RAY DIFFRACTION	c_scangle_it	5.634	2.5

Xplor file

Serial no: 1 / Param file: CNS_TOPPAR:protein_rep.param

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