PDB-2r7v: Crystal Structure of Rotavirus SA11 VP1/RNA (GGCUUU) Complex

ID or keywords:

Entry

Database: PDB / ID: 2r7v

Title

Crystal Structure of Rotavirus SA11 VP1/RNA (GGCUUU) Complex

Components

RNA (5'-R(*G*GP*CP*UP*UP*U)-3')
RNA-dependent RNA polymerase

Keywords

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

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 / Resolution: 2.8 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 10, 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
Revision 1.3	Feb 21, 2024	Group: Data collection / Database references Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	2r7v.cif.gz	232.3 KB	Display	PDBx/mmCIF format
PDB format	pdb2r7v.ent.gz	180.8 KB	Display	PDB format
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Validation report

Summary document	2r7v_validation.pdf.gz	461 KB	Display	wwPDB validaton report
Full document	2r7v_full_validation.pdf.gz	504.5 KB	Display
Data in XML	2r7v_validation.xml.gz	41.6 KB	Display
Data in CIF	2r7v_validation.cif.gz	57.4 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/r7/2r7v ftp://data.pdbj.org/pub/pdb/validation_reports/r7/2r7v	HTTPS FTP

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Related structure data

Related structure data	2r7oC 2r7qC 2r7rC 2r7sC 2r7tC 2r7uC 2r7wC 2r7xC C: citing same article (ref.)
Similar structure data	2r7u-d 2r7w-d 2r7o-d 2r7q-d 2r7s-d 2r7r-d 2r7x-2 2r7t-d 2r7x-1 6mez-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

X: RNA (5'-R(*G*GP*CP*UP*UP*U)-3')

A: RNA-dependent RNA polymerase

128 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author&software

Unit cell

Length a, b, c (Å)	76.452, 112.311, 143.719
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: RNA chain	RNA (5'-R(GGPCPUPUPU)-3') Mass: 1869.134 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: 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 details: pCRBac-based transfer vector (invitrogen) is used to produce VP1 gene integrated ACNPV Plasmid: pCRBac / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): sf21 / References: UniProt: O37061

#1: RNA chain

RNA (5'-R(*G*GP*CP*UP*UP*U)-3')

Mass: 1869.134 Da / Num. of mol.: 1 / Source method: obtained synthetically

#2: 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 details: pCRBac-based transfer vector (invitrogen) is used to produce VP1 gene integrated ACNPV
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: 2.42 Å³/Da / Density % sol: 49.22 %

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 ...

Components of the solutions

ID	Name	Crystal-ID	Sol-ID
1	Na-HEPES	1	1
2	NaCl	1	1
3	Na-MES	1	2
4	PEG 3350	1	2

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Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

ALS

/ Beamline: 8.2.1 / Wavelength: 1 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 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: 2.8→50 Å / Num. obs: 28572 / % possible obs: 91.4 % / Redundancy: 4.4 % / R_merge(I) obs: 0.065 / Χ²: 0.999 / Net I/σ(I): 17.1

Reflection shell

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Num. unique all	Χ²	% possible all
2.8-2.9	1.5	0.537	1464	1.002	47.6
2.9-3.02	2	0.439	2249	1.006	73.4
3.02-3.15	3.1	0.356	2833	1.005	92.4
3.15-3.32	4.1	0.264	3096	0.997	99.5
3.32-3.53	5	0.171	3073	0.997	99.9
3.53-3.8	5.1	0.112	3113	1	100
3.8-4.18	5.3	0.07	3114	0.998	100
4.18-4.79	5.2	0.051	3137	0.998	99.9
4.79-6.03	5.1	0.049	3162	0.999	99.7
6.03-50	4.9	0.025	3331	1	99.7

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Phasing

Phasing

Method:

MIRAS

Phasing set

ID
1
2
3
4
5
6
7
8
9

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

Phasing MIR

Resolution: 2.9→47.33 Å / FOM acentric: 0.284 / FOM centric: 0.202 / Reflection acentric: 24408 / Reflection centric: 2968

Phasing MIR der

Native set-ID: 1 / Resolution: 2.9→47.33 Å

ID	Der set-ID	Power acentric	Power centric	Reflection acentric	Reflection centric
ISO_1	1	0	0	16761	2059
ISO_2	2	0.309	0.29	13346	1743
ISO_3	3	0	0	14033	1746
ISO_4	4	0.344	0.334	13565	1708
ISO_5	5	0.261	0.237	11087	1473
ISO_6	6	0	0	11500	843
ISO_7	7	0.238	0.213	12088	884
ISO_8	8	0.248	0.224	11412	844
ISO_9	9	0.884	0.815	16487	1043

Phasing MIR der shell

Highest resolution (Å)	Lowest resolution (Å)	Der-ID	Power acentric	Power centric	Reflection acentric	Reflection centric
12.53	47.33	ISO_1	0	0	236	126
9.02	12.53	ISO_1	0	0	449	129
7.41	9.02	ISO_1	0	0	618	135
6.44	7.41	ISO_1	0	0	729	123
5.77	6.44	ISO_1	0	0	842	148
5.27	5.77	ISO_1	0	0	944	136
4.88	5.27	ISO_1	0	0	1031	129
4.57	4.88	ISO_1	0	0	1090	127
4.31	4.57	ISO_1	0	0	1167	125
4.09	4.31	ISO_1	0	0	1219	145
3.9	4.09	ISO_1	0	0	1251	127
3.74	3.9	ISO_1	0	0	1274	120
3.59	3.74	ISO_1	0	0	1303	116
3.46	3.59	ISO_1	0	0	1308	113
3.35	3.46	ISO_1	0	0	1351	110
3.24	3.35	ISO_1	0	0	1373	110
3.14	3.24	ISO_1	0	0	576	40
3.06	3.14	ISO_1	0	0	0	0
2.98	3.06	ISO_1	0	0	0	0
2.9	2.98	ISO_1	0	0	0	0
12.53	47.33	ISO_2	0.734	0.529	228	112
9.02	12.53	ISO_2	0.67	0.481	449	127
7.41	9.02	ISO_2	0.573	0.419	618	134
6.44	7.41	ISO_2	0.501	0.361	729	122
5.77	6.44	ISO_2	0.454	0.314	842	148
5.27	5.77	ISO_2	0.372	0.249	944	136
4.88	5.27	ISO_2	0.3	0.237	1030	128
4.57	4.88	ISO_2	0.242	0.183	1087	124
4.31	4.57	ISO_2	0.214	0.164	1141	122
4.09	4.31	ISO_2	0.185	0.124	1175	134
3.9	4.09	ISO_2	0.168	0.112	1200	117
3.74	3.9	ISO_2	0.15	0.104	1206	112
3.59	3.74	ISO_2	0.137	0.088	1225	108
3.46	3.59	ISO_2	0.118	0.072	1237	98
3.35	3.46	ISO_2	0.113	0.067	235	21
3.24	3.35	ISO_2	0	0	0	0
3.14	3.24	ISO_2	0	0	0	0
3.06	3.14	ISO_2	0	0	0	0
2.98	3.06	ISO_2	0	0	0	0
2.9	2.98	ISO_2	0	0	0	0
12.53	47.33	ISO_3	0	0	236	126
9.02	12.53	ISO_3	0	0	447	119
7.41	9.02	ISO_3	0	0	615	119
6.44	7.41	ISO_3	0	0	725	110
5.77	6.44	ISO_3	0	0	840	136
5.27	5.77	ISO_3	0	0	943	124
4.88	5.27	ISO_3	0	0	1031	119
4.57	4.88	ISO_3	0	0	1090	123
4.31	4.57	ISO_3	0	0	1167	123
4.09	4.31	ISO_3	0	0	1216	141
3.9	4.09	ISO_3	0	0	1250	127
3.74	3.9	ISO_3	0	0	1271	119
3.59	3.74	ISO_3	0	0	1290	107
3.46	3.59	ISO_3	0	0	1283	103
3.35	3.46	ISO_3	0	0	629	50
3.24	3.35	ISO_3	0	0	0	0
3.14	3.24	ISO_3	0	0	0	0
3.06	3.14	ISO_3	0	0	0	0
2.98	3.06	ISO_3	0	0	0	0
2.9	2.98	ISO_3	0	0	0	0
12.53	47.33	ISO_4	1.225	0.905	236	126
9.02	12.53	ISO_4	1.044	0.756	448	119
7.41	9.02	ISO_4	0.859	0.688	615	119
6.44	7.41	ISO_4	0.717	0.501	725	110
5.77	6.44	ISO_4	0.615	0.439	839	135
5.27	5.77	ISO_4	0.469	0.358	943	124
4.88	5.27	ISO_4	0.369	0.272	1031	119
4.57	4.88	ISO_4	0.303	0.22	1090	123
4.31	4.57	ISO_4	0.265	0.19	1166	123
4.09	4.31	ISO_4	0.224	0.128	1217	141
3.9	4.09	ISO_4	0.186	0.106	1247	127
3.74	3.9	ISO_4	0.153	0.1	1270	118
3.59	3.74	ISO_4	0.129	0.084	1291	108
3.46	3.59	ISO_4	0.102	0.066	1290	101
3.35	3.46	ISO_4	0.086	0.057	157	15
3.24	3.35	ISO_4	0	0	0	0
3.14	3.24	ISO_4	0	0	0	0
3.06	3.14	ISO_4	0	0	0	0
2.98	3.06	ISO_4	0	0	0	0
2.9	2.98	ISO_4	0	0	0	0
12.53	47.33	ISO_5	0.576	0.421	236	126
9.02	12.53	ISO_5	0.521	0.35	447	118
7.41	9.02	ISO_5	0.468	0.323	615	119
6.44	7.41	ISO_5	0.41	0.274	725	110
5.77	6.44	ISO_5	0.378	0.274	838	136
5.27	5.77	ISO_5	0.305	0.203	943	122
4.88	5.27	ISO_5	0.242	0.193	1031	115
4.57	4.88	ISO_5	0.189	0.15	1089	122
4.31	4.57	ISO_5	0.165	0.118	1163	122
4.09	4.31	ISO_5	0.143	0.092	1216	134
3.9	4.09	ISO_5	0.13	0.072	1241	122
3.74	3.9	ISO_5	0.104	0.069	1252	104
3.59	3.74	ISO_5	0.101	0.058	291	23
3.46	3.59	ISO_5	0	0	0	0
3.35	3.46	ISO_5	0	0	0	0
3.24	3.35	ISO_5	0	0	0	0
3.14	3.24	ISO_5	0	0	0	0
3.06	3.14	ISO_5	0	0	0	0
2.98	3.06	ISO_5	0	0	0	0
2.9	2.98	ISO_5	0	0	0	0
12.53	47.33	ISO_6	0	0	181	51
9.02	12.53	ISO_6	0	0	336	50
7.41	9.02	ISO_6	0	0	469	48
6.44	7.41	ISO_6	0	0	559	53
5.77	6.44	ISO_6	0	0	662	62
5.27	5.77	ISO_6	0	0	743	58
4.88	5.27	ISO_6	0	0	817	63
4.57	4.88	ISO_6	0	0	871	58
4.31	4.57	ISO_6	0	0	944	60
4.09	4.31	ISO_6	0	0	963	65
3.9	4.09	ISO_6	0	0	971	58
3.74	3.9	ISO_6	0	0	992	57
3.59	3.74	ISO_6	0	0	1000	58
3.46	3.59	ISO_6	0	0	959	49
3.35	3.46	ISO_6	0	0	777	41
3.24	3.35	ISO_6	0	0	256	12
3.14	3.24	ISO_6	0	0	0	0
3.06	3.14	ISO_6	0	0	0	0
2.98	3.06	ISO_6	0	0	0	0
2.9	2.98	ISO_6	0	0	0	0
12.53	47.33	ISO_7	0.776	0.438	182	52
9.02	12.53	ISO_7	0.608	0.462	337	51
7.41	9.02	ISO_7	0.543	0.31	470	48
6.44	7.41	ISO_7	0.466	0.3	559	53
5.77	6.44	ISO_7	0.408	0.292	662	62
5.27	5.77	ISO_7	0.322	0.264	745	58
4.88	5.27	ISO_7	0.255	0.198	817	63
4.57	4.88	ISO_7	0.208	0.151	873	59
4.31	4.57	ISO_7	0.176	0.123	948	61
4.09	4.31	ISO_7	0.147	0.083	980	69
3.9	4.09	ISO_7	0.134	0.076	1004	60
3.74	3.9	ISO_7	0.118	0.07	1034	58
3.59	3.74	ISO_7	0.105	0.061	1054	62
3.46	3.59	ISO_7	0.094	0.057	1061	58
3.35	3.46	ISO_7	0.072	0.051	1015	57
3.24	3.35	ISO_7	0.072	0.036	347	13
3.14	3.24	ISO_7	0	0	0	0
3.06	3.14	ISO_7	0	0	0	0
2.98	3.06	ISO_7	0	0	0	0
2.9	2.98	ISO_7	0	0	0	0
12.53	47.33	ISO_8	0.785	0.438	180	51
9.02	12.53	ISO_8	0.588	0.415	335	50
7.41	9.02	ISO_8	0.517	0.316	469	49
6.44	7.41	ISO_8	0.459	0.3	558	53
5.77	6.44	ISO_8	0.394	0.332	661	62
5.27	5.77	ISO_8	0.323	0.234	743	58
4.88	5.27	ISO_8	0.248	0.222	816	63
4.57	4.88	ISO_8	0.202	0.153	868	59
4.31	4.57	ISO_8	0.18	0.129	937	58
4.09	4.31	ISO_8	0.142	0.081	957	67
3.9	4.09	ISO_8	0.136	0.081	960	58
3.74	3.9	ISO_8	0.12	0.08	980	58
3.59	3.74	ISO_8	0.109	0.059	996	54
3.46	3.59	ISO_8	0.096	0.058	950	53
3.35	3.46	ISO_8	0.079	0.055	766	40
3.24	3.35	ISO_8	0.074	0.035	236	11
3.14	3.24	ISO_8	0	0	0	0
3.06	3.14	ISO_8	0	0	0	0
2.98	3.06	ISO_8	0	0	0	0
2.9	2.98	ISO_8	0	0	0	0
12.53	47.33	ISO_9	1.845	1.389	228	56
9.02	12.53	ISO_9	1.483	0.966	449	63
7.41	9.02	ISO_9	1.372	1.026	618	72
6.44	7.41	ISO_9	1.346	1.024	728	62
5.77	6.44	ISO_9	1.228	0.807	842	77
5.27	5.77	ISO_9	1.028	0.75	943	68
4.88	5.27	ISO_9	0.805	0.739	1027	62
4.57	4.88	ISO_9	0.651	0.447	1082	66
4.31	4.57	ISO_9	0.551	0.358	1149	65
4.09	4.31	ISO_9	0.486	0.274	1205	75
3.9	4.09	ISO_9	0.44	0.243	1216	66
3.74	3.9	ISO_9	0.395	0.306	1242	63
3.59	3.74	ISO_9	0.364	0.29	1265	56
3.46	3.59	ISO_9	0.332	0.243	1282	61
3.35	3.46	ISO_9	0.305	0.252	1315	56
3.24	3.35	ISO_9	0.296	0.256	1341	49
3.14	3.24	ISO_9	0.292	0.154	555	26
3.06	3.14	ISO_9	0	0	0	0
2.98	3.06	ISO_9	0	0	0	0
2.9	2.98	ISO_9	0	0	0	0

Phasing MIR 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

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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
HKL-2000		data scaling

Refinement

Method to determine structure:

MIRAS / Resolution: 2.8→50 Å / σ(F): 0

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.279	2130	6.8 %	RANDOM
R_work	0.228	-	-	-
obs	-	26782	85.9 %	-

Solvent computation

B_sol: 34.563 Å²

Displacement parameters

B_iso mean: 56.937 Å²

Refinement step

Cycle: LAST / Resolution: 2.8→50 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	8699	100	0	0	8799

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target
X-RAY DIFFRACTION	c_mcbond_it	1.704	1.5
X-RAY DIFFRACTION	c_scbond_it	2.408	2
X-RAY DIFFRACTION	c_mcangle_it	2.99	2
X-RAY DIFFRACTION	c_scangle_it	4.055	2.5

Xplor file

Refine-ID	Serial no	Param file
X-RAY DIFFRACTION	1	CNS_TOPPAR:protein_rep.param
X-RAY DIFFRACTION	2	CNS_TOPPAR:ion.param
X-RAY DIFFRACTION	3	CNS_TOPPAR:dna-rna_rep.param

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