PDB-3drf: Lactococcal OppA complexed with an endogenous peptide in the clos...

ID or keywords:

Entry

Database: PDB / ID: 3drf

Title

Lactococcal OppA complexed with an endogenous peptide in the closed conformation

Components

Oligopeptide-binding protein oppA
endogenous peptide

Keywords

PEPTIDE BINDING PROTEIN / oligo-peptide binding / voluminous binding cavity /

venus fly-trap

Function / homology

Function and homology information

peptide transport / ATP-binding cassette (ABC) transporter complex / transmembrane transport /

protein transport /

periplasmic space
Similarity search - Function

Biological species

Lactococcus lactis (lactic acid bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MAD / Resolution: 1.3 Å

Authors

Berntsson, R.P.-A. / Doeven, M.K. / Duurkens, R.H. / Sengupta, D. / Marrink, S.-J. / Thunnissen, A.-M. / Poolman, B. / Slotboom, D.-J.

Citation

Journal: Embo J. / Year: 2009
Title: The structural basis for peptide selection by the transport receptor OppA
Authors: Berntsson, R.P.-A. / Doeven, M.K. / Fusetti, F. / Duurkens, R.H. / Sengupta, D. / Marrink, S.-J. / Thunnissen, A.-M. / Poolman, B. / Slotboom, D.-J.

History

Deposition	Jul 11, 2008	Deposition site: RCSB / Processing site: PDBJ
Revision 1.0	Mar 31, 2009	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Version format compliance
Revision 1.2	Feb 5, 2014	Group: Database references
Revision 1.3	Mar 20, 2024	Group: Data collection / Database references Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	3drf.cif.gz	271.4 KB	Display	PDBx/mmCIF format
PDB format	pdb3drf.ent.gz	214 KB	Display	PDB format
PDBx/mmJSON format	3drf.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/dr/3drf ftp://data.pdbj.org/pub/pdb/validation_reports/dr/3drf	HTTPS FTP

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Related structure data

Related structure data	3drgC 3drhC 3driC 3drjC 3drkC C: citing same article (ref.)
Similar structure data	1qyx-1 1qyw-1 1fdu-2 3e3k-3 3klp-1 4pfw-1 1fds-1 6lzu-d 6mnc-d 6f73-2 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
Related items in Molecule of the Month	#261 - Sep 2021 DNA-Sequencing Nanopores similarity (1) #22 - Oct 2001 Photosystem I similarity (1) #262 - Oct 2021 Fifty Years of Open Access to PDB Structures similarity (1) #29 - May 2002 Penicillin-binding Proteins similarity (1) #95 - Nov 2007 Multidrug Resistance Transporters similarity (1)

Deposited unit

A: Oligopeptide-binding protein oppA

B: endogenous peptide

65.9 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)	59.114, 74.650, 115.445
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein	Oligopeptide-binding protein oppA Mass: 65144.773 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: Construct lacking N-terminal signal sequence and cysteine used for lipid modification Source: (gene. exp.) Lactococcus lactis (lactic acid bacteria) Strain: subsp. cremoris MG1363 / Gene: oppA, llmg_0701 / Plasmid: pAMP21 / Production host: Lactococcus lactis (lactic acid bacteria) / Strain (production host): MG1363 / References: UniProt: A2RJ53
#2: Protein/peptide	endogenous peptide Mass: 705.717 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: chemically synthesis
#3: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 1119 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 3

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Sample preparation

Crystal	Density Matthews: 2.11 Å³/Da / Density % sol: 36.430637 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 0.2M NaCl, 0.1M Na-Hepes, pH 7.0, 20% PEG 6000, vapor diffusion, hanging drop, temperature 293K

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Data collection

Diffraction

ID	Mean temperature (K)	Crystal-ID
1	100	1
2	100	1
3	100	1

Diffraction source

Source	Site	Beamline	ID	Wavelength (Å)
SYNCHROTRON	ESRF	BM16	1	0.999
SYNCHROTRON	ESRF	ID29	2	0.9197, 0.9199, 0.9168
SYNCHROTRON	ESRF	ID29	3	1.775

Detector

Type	ID	Detector	Date
ADSC Q210r	1	CCD	Feb 18, 2007
ADSC Q315R	2	CCD	Feb 18, 2007
ADSC Q315R	3	CCD	Feb 18, 2007

Radiation

ID	Protocol	Monochromatic (M) / Laue (L)	Scattering type	Wavelength-ID
1	SINGLE WAVELENGTH	M	x-ray	1
2	MAD	M	x-ray	1
3	SINGLE WAVELENGTH	M	x-ray	1

Radiation wavelength

ID	Wavelength (Å)	Relative weight
1	0.999	1
2	0.9197	1
3	0.9199	1
4	0.9168	1
5	1.775	1

Reflection

Highest resolution: 1.3 Å / Num. obs: 124464 / % possible obs: 99.4 % / Observed criterion σ(I): -3 / B_iso Wilson estimate: 14.587 Å² / R_merge(I) obs: 0.053 / Net I/σ(I): 19.61

Reflection shell

Diffraction-ID: 1,2,3

Resolution (Å)	Highest resolution (Å)	R_merge(I) obs	Mean I/σ(I) obs	Num. measured obs	Num. unique obs	% possible all
1.3-1.38		0.364	4.3	89413	19582	97.9
1.38-1.47		0.256	6.1	88896	18810	100
1.47-1.59		0.167	9.2	83675	17533	100
1.59-1.74		0.111	13.4	77930	16197	99.9
1.74-1.94		0.068	20.3	71054	14700	99.9
1.94-2.24		0.043	30.8	63072	13025	99.9
2.24-2.74		0.033	39.6	53609	11052	99.6
2.74-3.85		0.024	50.6	41770	8629	99.1
	3.85	0.02	58.6	22977	4935	96.2

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Phasing

Phasing

Method:

MAD

Phasing MAD set

ID	Highest resolution (Å)	Lowest resolution (Å)	Power acentric	Power centric	Reflection acentric	Reflection centric
ISO_1	2.3	46.13	0	0	19138	2390
ISO_2	2.3	46.13	0.551	0.469	19133	2105
ISO_3	2.3	46.13	0.214	0.184	19131	2374
ISO_4	2.3	46.13	0.76	0.663	14935	1905
ISO_5	2.3	46.13	0.841	0.732	19071	1880
ANO_1	2.3	46.13	1.27	0	18607	0
ANO_2	2.3	46.13	0.654	0	18603	0
ANO_3	2.3	46.13	0.83	0	18602	0
ANO_4	2.3	46.13	0.215	0	15061	0
ANO_5	2.3	46.13	0.174	0	19093	0

Phasing MAD set shell

ID	Resolution (Å)	Power acentric	Power centric	Reflection acentric	Reflection centric
ISO_1	10.05-46.13	0	0	168	91
ISO_1	7.19-10.05	0	0	362	128
ISO_1	5.9-7.19	0	0	497	116
ISO_1	5.12-5.9	0	0	598	136
ISO_1	4.58-5.12	0	0	672	120
ISO_1	4.19-4.58	0	0	743	128
ISO_1	3.88-4.19	0	0	823	127
ISO_1	3.63-3.88	0	0	884	118
ISO_1	3.42-3.63	0	0	939	115
ISO_1	3.25-3.42	0	0	996	124
ISO_1	3.1-3.25	0	0	1047	103
ISO_1	2.97-3.1	0	0	1112	119
ISO_1	2.85-2.97	0	0	1169	123
ISO_1	2.75-2.85	0	0	1198	122
ISO_1	2.65-2.75	0	0	1246	130
ISO_1	2.57-2.65	0	0	1290	128
ISO_1	2.49-2.57	0	0	1349	119
ISO_1	2.42-2.49	0	0	1414	120
ISO_1	2.36-2.42	0	0	1437	121
ISO_1	2.3-2.36	0	0	1194	102
ANO_1	10.05-46.13	2.569	0	168	0
ANO_1	7.19-10.05	2.908	0	361	0
ANO_1	5.9-7.19	2.992	0	496	0
ANO_1	5.12-5.9	2.875	0	598	0
ANO_1	4.58-5.12	2.251	0	671	0
ANO_1	4.19-4.58	1.875	0	732	0
ANO_1	3.88-4.19	1.504	0	792	0
ANO_1	3.63-3.88	1.39	0	850	0
ANO_1	3.42-3.63	1.368	0	893	0
ANO_1	3.25-3.42	1.449	0	942	0
ANO_1	3.1-3.25	1.333	0	988	0
ANO_1	2.97-3.1	1.304	0	1058	0
ANO_1	2.85-2.97	1.209	0	1111	0
ANO_1	2.75-2.85	1.084	0	1144	0
ANO_1	2.65-2.75	0.954	0	1205	0
ANO_1	2.57-2.65	0.833	0	1249	0
ANO_1	2.49-2.57	0.776	0	1322	0
ANO_1	2.42-2.49	0.674	0	1406	0
ANO_1	2.36-2.42	0.592	0	1429	0
ANO_1	2.3-2.36	0.552	0	1192	0
ISO_2	10.05-46.13	0.556	0.515	168	86
ISO_2	7.19-10.05	0.989	0.824	362	125
ISO_2	5.9-7.19	1.061	0.891	497	114
ISO_2	5.12-5.9	0.818	0.588	598	130
ISO_2	4.58-5.12	0.728	0.653	672	115
ISO_2	4.19-4.58	0.662	0.576	743	101
ISO_2	3.88-4.19	0.638	0.427	822	65
ISO_2	3.63-3.88	0.614	0.588	884	102
ISO_2	3.42-3.63	0.565	0.426	939	98
ISO_2	3.25-3.42	0.567	0.384	996	107
ISO_2	3.1-3.25	0.532	0.44	1047	86
ISO_2	2.97-3.1	0.542	0.365	1110	107
ISO_2	2.85-2.97	0.5	0.363	1168	111
ISO_2	2.75-2.85	0.478	0.327	1198	110
ISO_2	2.65-2.75	0.448	0.316	1246	117
ISO_2	2.57-2.65	0.41	0.291	1290	113
ISO_2	2.49-2.57	0.382	0.282	1349	109
ISO_2	2.42-2.49	0.346	0.218	1414	111
ISO_2	2.36-2.42	0.313	0.198	1436	107
ISO_2	2.3-2.36	0.289	0.208	1194	91
ANO_2	10.05-46.13	1.607	0	168	0
ANO_2	7.19-10.05	1.652	0	361	0
ANO_2	5.9-7.19	1.991	0	496	0
ANO_2	5.12-5.9	1.484	0	598	0
ANO_2	4.58-5.12	1.074	0	671	0
ANO_2	4.19-4.58	0.852	0	732	0
ANO_2	3.88-4.19	0.744	0	793	0
ANO_2	3.63-3.88	0.723	0	851	0
ANO_2	3.42-3.63	0.671	0	893	0
ANO_2	3.25-3.42	0.695	0	942	0
ANO_2	3.1-3.25	0.608	0	989	0
ANO_2	2.97-3.1	0.621	0	1056	0
ANO_2	2.85-2.97	0.603	0	1114	0
ANO_2	2.75-2.85	0.556	0	1143	0
ANO_2	2.65-2.75	0.488	0	1206	0
ANO_2	2.57-2.65	0.463	0	1247	0
ANO_2	2.49-2.57	0.412	0	1321	0
ANO_2	2.42-2.49	0.352	0	1404	0
ANO_2	2.36-2.42	0.322	0	1426	0
ANO_2	2.3-2.36	0.312	0	1192	0
ISO_3	10.05-46.13	0.341	0.288	168	90
ISO_3	7.19-10.05	0.444	0.35	362	127
ISO_3	5.9-7.19	0.446	0.321	497	116
ISO_3	5.12-5.9	0.371	0.273	598	135
ISO_3	4.58-5.12	0.313	0.285	672	119
ISO_3	4.19-4.58	0.29	0.21	743	127
ISO_3	3.88-4.19	0.266	0.2	821	124
ISO_3	3.63-3.88	0.251	0.237	884	117
ISO_3	3.42-3.63	0.227	0.169	939	114
ISO_3	3.25-3.42	0.218	0.148	996	123
ISO_3	3.1-3.25	0.211	0.171	1046	102
ISO_3	2.97-3.1	0.197	0.137	1111	117
ISO_3	2.85-2.97	0.181	0.131	1169	123
ISO_3	2.75-2.85	0.173	0.125	1197	122
ISO_3	2.65-2.75	0.16	0.116	1246	130
ISO_3	2.57-2.65	0.148	0.105	1290	128
ISO_3	2.49-2.57	0.141	0.104	1348	119
ISO_3	2.42-2.49	0.127	0.073	1414	118
ISO_3	2.36-2.42	0.112	0.077	1436	121
ISO_3	2.3-2.36	0.107	0.078	1194	102
ANO_3	10.05-46.13	2.092	0	168	0
ANO_3	7.19-10.05	2.345	0	360	0
ANO_3	5.9-7.19	2.779	0	496	0
ANO_3	5.12-5.9	2.337	0	598	0
ANO_3	4.58-5.12	1.774	0	670	0
ANO_3	4.19-4.58	1.486	0	732	0
ANO_3	3.88-4.19	1.216	0	795	0
ANO_3	3.63-3.88	1.12	0	849	0
ANO_3	3.42-3.63	0.964	0	892	0
ANO_3	3.25-3.42	0.935	0	938	0
ANO_3	3.1-3.25	0.952	0	986	0
ANO_3	2.97-3.1	0.884	0	1058	0
ANO_3	2.85-2.97	0.772	0	1113	0
ANO_3	2.75-2.85	0.75	0	1144	0
ANO_3	2.65-2.75	0.582	0	1207	0
ANO_3	2.57-2.65	0.54	0	1253	0
ANO_3	2.49-2.57	0.476	0	1322	0
ANO_3	2.42-2.49	0.422	0	1404	0
ANO_3	2.36-2.42	0.337	0	1426	0
ANO_3	2.3-2.36	0.314	0	1191	0
ISO_4	10.05-46.13	1.753	1.314	168	88
ISO_4	7.19-10.05	1.882	1.205	362	126
ISO_4	5.9-7.19	1.711	1.419	497	116
ISO_4	5.12-5.9	1.582	1.137	598	133
ISO_4	4.58-5.12	1.277	1.099	672	117
ISO_4	4.19-4.58	1.04	0.732	743	116
ISO_4	3.88-4.19	0.873	0.532	823	96
ISO_4	3.63-3.88	0.709	0.581	884	111
ISO_4	3.42-3.63	0.635	0.426	939	105
ISO_4	3.25-3.42	0.588	0.381	996	116
ISO_4	3.1-3.25	0.551	0.412	1047	95
ISO_4	2.97-3.1	0.551	0.379	1112	112
ISO_4	2.85-2.97	0.539	0.409	1169	119
ISO_4	2.75-2.85	0.531	0.354	1198	115
ISO_4	2.65-2.75	0.5	0.416	1246	123
ISO_4	2.57-2.65	0.488	0.348	1289	118
ISO_4	2.49-2.57	0.447	0.355	1192	99
ISO_4	2.42-2.49	0	0	0	0
ISO_4	2.36-2.42	0	0	0	0
ISO_4	2.3-2.36	0	0	0	0
ANO_4	10.05-46.13	0.535	0	173	0
ANO_4	7.19-10.05	0.668	0	362	0
ANO_4	5.9-7.19	0.607	0	498	0
ANO_4	5.12-5.9	0.546	0	601	0
ANO_4	4.58-5.12	0.412	0	674	0
ANO_4	4.19-4.58	0.338	0	748	0
ANO_4	3.88-4.19	0.286	0	831	0
ANO_4	3.63-3.88	0.278	0	891	0
ANO_4	3.42-3.63	0.282	0	947	0
ANO_4	3.25-3.42	0.243	0	1002	0
ANO_4	3.1-3.25	0.227	0	1054	0
ANO_4	2.97-3.1	0.185	0	1127	0
ANO_4	2.85-2.97	0.152	0	1183	0
ANO_4	2.75-2.85	0.146	0	1221	0
ANO_4	2.65-2.75	0.111	0	1246	0
ANO_4	2.57-2.65	0.096	0	1300	0
ANO_4	2.49-2.57	0.082	0	1203	0
ANO_4	2.42-2.49	0	0	0	0
ANO_4	2.36-2.42	0	0	0	0
ANO_4	2.3-2.36	0	0	0	0
ISO_5	10.05-46.13	1.772	1.251	164	67
ISO_5	7.19-10.05	1.921	1.354	357	100
ISO_5	5.9-7.19	1.795	1.531	492	96
ISO_5	5.12-5.9	1.688	1.149	590	113
ISO_5	4.58-5.12	1.418	1.157	665	94
ISO_5	4.19-4.58	1.199	0.832	740	98
ISO_5	3.88-4.19	1.056	0.681	817	73
ISO_5	3.63-3.88	0.836	0.753	879	91
ISO_5	3.42-3.63	0.771	0.53	936	88
ISO_5	3.25-3.42	0.719	0.469	992	98
ISO_5	3.1-3.25	0.712	0.506	1043	83
ISO_5	2.97-3.1	0.677	0.544	1107	94
ISO_5	2.85-2.97	0.69	0.514	1166	99
ISO_5	2.75-2.85	0.654	0.478	1197	98
ISO_5	2.65-2.75	0.619	0.502	1245	109
ISO_5	2.57-2.65	0.583	0.39	1289	99
ISO_5	2.49-2.57	0.56	0.452	1348	99
ISO_5	2.42-2.49	0.479	0.347	1413	95
ISO_5	2.36-2.42	0.434	0.303	1437	103
ISO_5	2.3-2.36	0.405	0.291	1194	83
ANO_5	10.05-46.13	0.199	0	157	0
ANO_5	7.19-10.05	0.315	0	347	0
ANO_5	5.9-7.19	0.382	0	475	0
ANO_5	5.12-5.9	0.327	0	571	0
ANO_5	4.58-5.12	0.258	0	639	0
ANO_5	4.19-4.58	0.261	0	718	0
ANO_5	3.88-4.19	0.214	0	798	0
ANO_5	3.63-3.88	0.206	0	852	0
ANO_5	3.42-3.63	0.202	0	916	0
ANO_5	3.25-3.42	0.173	0	965	0
ANO_5	3.1-3.25	0.174	0	1016	0
ANO_5	2.97-3.1	0.171	0	1091	0
ANO_5	2.85-2.97	0.153	0	1152	0
ANO_5	2.75-2.85	0.142	0	1198	0
ANO_5	2.65-2.75	0.139	0	1226	0
ANO_5	2.57-2.65	0.125	0	1281	0
ANO_5	2.49-2.57	0.115	0	1352	0
ANO_5	2.42-2.49	0.101	0	1408	0
ANO_5	2.36-2.42	0.096	0	1435	0
ANO_5	2.3-2.36	0.082	0	1496	0

Phasing MAD set site

ID	Cartn x (Å)	Cartn y (Å)	Cartn z (Å)	Atom type symbol	B iso	Occupancy
1	-53.917	-33.554	-2.952	BR	30	0.95
2	-45.515	-33.556	-27.193	BR	30	0.67
3	-45.182	-11.281	-18.132	BR	30	0.64
4	-49.218	-58.323	-9.412	BR	30	0.97
5	-42.325	-10.923	-36.652	BR	30	0.34
6	-37.482	11.21	-43.905	BR	30	0.47
7	-34.778	-63.488	-3.439	BR	30	0.54
8	-29.091	4.355	-60.649	BR	30	0.51
9	-31.526	-30.945	-31.943	BR	30	0.51
10	-38.966	-25.392	-40.145	BR	30	0.56
11	-28.743	-4.17	-57.496	BR	30	0.19
12	-40.329	-14.59	-22.388	BR	30	0.6
13	-35.995	-70.295	-14.016	BR	30	0.33
14	-52.302	-32.819	-25.406	BR	30	0.42
15	-42.982	-45.511	-4.1	BR	30	0.42
16	-22.827	-0.109	-28.451	BR	30	0.55
17	-36.569	-70.042	-16.763	BR	30	0.34
18	-41.964	-3.831	-8.259	BR	30	0.2
19	-44.971	-5.123	-22.955	BR	30	0.4
20	-0.626	-29.115	-3.306	BR	30	0.26
21	32.215	38.258	41.436	BR	30	0.66
22	45.126	9.287	14.547	S	30	0.34
23	34.185	71.546	3.379	S	30	0.69
24	57.484	25.771	24.738	S	30	0.34
25	34.632	39.569	28.598	S	30	0.32
26	47.721	51.287	22.017	S	30	0.66
27	20.649	57.97	47.358	S	30	0.64
28	29.454	22.922	99.665	S	30	0.4
29	57.915	33.821	85.659	S	30	0.37
30	27.256	0.526	16.046	S	30	0.64
31	11.655	36.488	71.078	S	30	0.31
32	23.753	66.054	98.604	S	30	0.26
33	54.412	16.791	43.702	S	30	0.25
34	7.166	58.977	35.217	S	30	0.3
35	53.856	3.023	61.031	HG	30	0.1
36	50.074	53.611	68.04	HG	30	0.08
37	27.35	0.865	16.02	HG	30	0.09
38	18.208	60.522	92.915	HG	30	0.08

Phasing dm

FOM : 0.75 / FOM acentric: 0.77 / FOM centric: 0.65 / Reflection: 22875 / Reflection acentric: 20091 / Reflection centric: 2784

Phasing dm shell

Resolution (Å)	FOM	FOM acentric	FOM centric	Reflection	Reflection acentric	Reflection centric
6.6-57.514	0.87	0.91	0.8	1094	757	337
4.1-6.6	0.88	0.9	0.77	3140	2592	548
3.3-4.1	0.86	0.87	0.75	3877	3376	501
2.9-3.3	0.79	0.81	0.65	3859	3449	410
2.5-2.9	0.69	0.71	0.53	6781	6140	641
2.3-2.5	0.6	0.62	0.42	4124	3777	347

-
Processing

Software

Name	Version	Classification
XSCALE		data scaling
SHARP		phasing
RESOLVE	2.13	phasing
REFMAC		refinement
PDB_EXTRACT	3.005	data extraction

Refinement

Method to determine structure:

MAD / Resolution: 1.3→62.75 Å / Cor.coef. F_o:F_c: 0.976 / Cor.coef. F_o:F_c free: 0.966 / SU B: 1.354 / SU ML: 0.027 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.049 / ESU R Free: 0.046 / Stereochemistry target values: MAXIMUM LIKELIHOOD

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.16147	6300	5 %	RANDOM
R_work	0.13132	-	-	-
obs	0.13286	119254	99.64 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK

Displacement parameters

B_iso mean: 8.442 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.03 Å²	-0 Å²	0 Å²
2-	-	-0.2 Å²	-0 Å²
3-	-	-	0.17 Å²

Refinement step

Cycle: LAST / Resolution: 1.3→62.75 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4249	0	0	1119	5368

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.009	0.022	4519
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.02	3015
X-RAY DIFFRACTION	r_angle_refined_deg	1.29	1.951	6151
X-RAY DIFFRACTION	r_angle_other_deg	0.859	3	7430
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.597	5	585
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	37.259	25.879	199
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	10.93	15	768
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	16.57	15	9
X-RAY DIFFRACTION	r_chiral_restr	0.079	0.2	656
X-RAY DIFFRACTION	r_gen_planes_refined	0.006	0.021	5174
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	873
X-RAY DIFFRACTION	r_nbd_refined
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined
X-RAY DIFFRACTION	r_xyhbond_nbd_other
X-RAY DIFFRACTION	r_metal_ion_refined
X-RAY DIFFRACTION	r_metal_ion_other
X-RAY DIFFRACTION	r_symmetry_vdw_refined
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined
X-RAY DIFFRACTION	r_symmetry_hbond_other
X-RAY DIFFRACTION	r_symmetry_metal_ion_refined
X-RAY DIFFRACTION	r_symmetry_metal_ion_other
X-RAY DIFFRACTION	r_mcbond_it	0.859	1.5	2838
X-RAY DIFFRACTION	r_mcbond_other	0.339	1.5	1153
X-RAY DIFFRACTION	r_mcangle_it	1.381	2	4591
X-RAY DIFFRACTION	r_scbond_it	2.051	3	1681
X-RAY DIFFRACTION	r_scangle_it	3.074	4.5	1560
X-RAY DIFFRACTION	r_rigid_bond_restr	0.879	3	7534
X-RAY DIFFRACTION	r_sphericity_free	4.051	3	1117
X-RAY DIFFRACTION	r_sphericity_bonded	1.803	3	7418

LS refinement shell

Resolution: 1.3→1.334 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.201	462	-
R_work	0.17	8811	-
all	-	9273	-
obs	-	-	100 %

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