PDB-2atf: X-RAY STRUCTURE OF cysteine dioxygenase type I FROM MUS MUSCULUS ...

ID or keywords:

Entry

Database: PDB / ID: 2atf

Title

X-RAY STRUCTURE OF cysteine dioxygenase type I FROM MUS MUSCULUS MM.241056

Components

Cysteine dioxygenase type I

Keywords

OXIDOREDUCTASE / Mm.241056 / pfam05995.2 CDO_I / BC013638 / CUPIN FAMILY / STRUCTURAL GENOMICS / PROTEIN STRUCTURE INITIATIVE / PSI / Center for Eukaryotic Structural Genomics / CESG

Function / homology

Function and homology information

: / Degradation of cysteine and homocysteine / taurine metabolic process / taurine biosynthetic process / cysteine dioxygenase / cysteine dioxygenase activity / response to azide / L-cysteine catabolic process / response to glucagon / nickel cation binding ...
Similarity search - Function

Biological species

Mus musculus (house mouse)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MAD / Resolution: 1.75 Å

Authors

Wesenberg, G.E. / Phillips Jr., G.N. / Mccoy, J.G. / Bitto, E. / Bingman, C.A. / Allard, S.T.M. / Center for Eukaryotic Structural Genomics (CESG)

Citation

Journal: Proc.Natl.Acad.Sci.Usa / Year: 2006
Title: Structure and mechanism of mouse cysteine dioxygenase.
Authors: McCoy, J.G. / Bailey, L.J. / Bitto, E. / Bingman, C.A. / Aceti, D.J. / Fox, B.G. / Phillips, G.N.

History

Deposition	Aug 24, 2005	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Oct 18, 2005	Provider: repository / Type: Initial release
Revision 1.1	Oct 16, 2007	Group: Version format compliance
Revision 1.2	Jul 13, 2011	Group: Version format compliance
Revision 1.3	Oct 11, 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 1.4	Oct 30, 2024	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / struct_conn / struct_conn_type / struct_ref_seq_dif / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn_type.id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	2atf.cif.gz	62 KB	Display	PDBx/mmCIF format
PDB format	pdb2atf.ent.gz	42.1 KB	Display	PDB format
PDBx/mmJSON format	2atf.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/at/2atf ftp://data.pdbj.org/pub/pdb/validation_reports/at/2atf	HTTPS FTP

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Related structure data

Similar structure data	4piy-d 4iez-d 5efu-d 4iev-d 4xfi-d 4ies-d 4ubh-d 4z82-d 4kwl-d 5i0u-d 2q4s-d 4xf0-d 4piz-d 6u4l-d 5ezw-d 2gh2-d 4xf3-d 4yyo-d 4kwk-d 4iet-d Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search
Other databases	TargetDB: GO.35683

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Cysteine dioxygenase type I

hetero molecules

23.3 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)	57.550, 57.550, 122.076
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	96
Space group name H-M	P4₃2₁2

#1: Protein	Cysteine dioxygenase type I / CDO / CDO-I Mass: 23155.457 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Cdo1 / Plasmid: PVP 16 / Production host: Escherichia coli (E. coli) / Strain (production host): B834 P(RARE2) / References: UniProt: P60334, cysteine dioxygenase
#2: Chemical	ChemComp-NI / NICKEL (II) ION Mass: 58.693 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ni
#3: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₂H₆O₂
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 188 / Source method: isolated from a natural source / Formula: H₂O
Has protein modification	Y
Nonpolymer details	The metal ion in this structure is currently modeled as Ni2+.ICP analysis indicates that there is a ...The metal ion in this structure is currently modeled as Ni2+.ICP analysis indicates that there is a mixture of metals in the protein sample, with Ni dominant, Zn next most abundant, and some Fe. The biologically relevant metal ion is expected to be Fe2+.

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.2 Å³/Da / Density % sol: 43.6 %
Crystal grow	Temperature: 273 K / Method: vapor diffusion, hanging drop / pH: 6 Details: 10 MG/ML PROTEIN, 20% MPEG 5K, 0.16 M CALCIUM CHLORIDE, 0.10 M MES, pH 6.0, vapor diffusion, hanging drop, temperature 273K

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Data collection

Diffraction

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

Diffraction source

Source:

SYNCHROTRON / Site:

APS

/ Beamline: 23-ID-D / Wavelength: 0.97915, 0.97933, 0.96392

Detector

Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Aug 9, 2005
Details: PAIR OF BIMORPH, RHODIUM COATED KIRKPATRICK-BAEZ MIRRORS

Radiation

Monochromator: INDIRECT LIQUID NITROGEN COOLED DOUBLE CRYSTAL MONOCHROMATOR WITH SI-111 CRYSTALS
Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

ID	Wavelength (Å)	Relative weight
1	0.97915	1
2	0.97933	1
3	0.96392	1

Reflection

D res high: 1.75 Å / D res low: 50 Å / % possible obs: 100

Redundancy (%)	ID	Number	R_merge(I) obs	Χ²
14.2	1	21529	0.118	1.427
14.2	2	21553	0.109	1.051
14.3	3	21554	0.108	1.026

Diffraction reflection shell

Highest resolution (Å)	Lowest resolution (Å)	% possible obs (%)	ID	R_merge(I) obs	Chi squared	Redundancy
4.32	50	99.9	1	0.105	2.204	12.9
3.43	4.32	100	1	0.103	2.053	14
2.99	3.43	100	1	0.108	2.189	14.1
2.72	2.99	100	1	0.119	2.224	14.3
2.52	2.72	100	1	0.121	1.782	14.4
2.38	2.52	100	1	0.129	1.568	14.4
2.26	2.38	100	1	0.137	1.591	14.5
2.16	2.26	100	1	0.136	1.582	14.5
2.07	2.16	100	1	0.143	1.286	14.4
2	2.07	100	1	0.149	1.191	14.4
1.94	2	100	1	0.156	1.016	14.5
1.89	1.94	100	1	0.172	0.817	14.5
1.84	1.89	100	1	0.199	0.685	14.5
1.79	1.84	100	1	0.225	0.597	14.4
1.75	1.79	100	1	0.27	0.519	13.8
4.32	50	99.9	2	0.095	1.069	12.9
3.43	4.32	100	2	0.097	1.077	14
2.99	3.43	100	2	0.104	0.995	14.2
2.72	2.99	100	2	0.109	1.006	14.4
2.52	2.72	100	2	0.11	1.031	14.4
2.38	2.52	100	2	0.116	1.033	14.4
2.26	2.38	100	2	0.125	1.031	14.5
2.16	2.26	100	2	0.127	1.094	14.5
2.07	2.16	100	2	0.135	1.059	14.5
2	2.07	100	2	0.137	1.085	14.5
1.94	2	100	2	0.148	1.095	14.5
1.89	1.94	100	2	0.168	1.1	14.4
1.84	1.89	100	2	0.198	1.086	14.5
1.79	1.84	100	2	0.227	1.049	14.3
1.75	1.79	100	2	0.283	0.951	13.4
4.32	50	99.9	3	0.096	1.001	12.9
3.43	4.32	100	3	0.096	0.944	14
2.99	3.43	100	3	0.102	0.903	14.2
2.72	2.99	100	3	0.109	1.055	14.4
2.52	2.72	100	3	0.109	1.056	14.4
2.38	2.52	100	3	0.115	1.045	14.4
2.26	2.38	100	3	0.122	0.968	14.5
2.16	2.26	100	3	0.126	1.06	14.5
2.07	2.16	100	3	0.132	1.078	14.5
2	2.07	100	3	0.135	1.053	14.5
1.94	2	100	3	0.143	1.07	14.5
1.89	1.94	100	3	0.157	1.074	14.5
1.84	1.89	100	3	0.183	1.077	14.5
1.79	1.84	100	3	0.207	1.068	14.5
1.75	1.79	100	3	0.257	0.941	14.3

Reflection

Resolution: 1.75→50 Å / Num. obs: 21529 / % possible obs: 100 % / Redundancy: 14.2 % / R_merge(I) obs: 0.118 / Net I/σ(I): 15.888

Reflection shell

Resolution: 1.75→1.79 Å / Redundancy: 13.8 % / R_merge(I) obs: 0.27 / Mean I/σ(I) obs: 5.25 / % possible all: 100

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Phasing

Phasing

Method:

MAD

Phasing MAD set

Highest resolution: 1.75 Å / Lowest resolution: 33.86 Å

ID	R cullis acentric	R cullis centric	Power acentric	Power centric	Reflection acentric	Reflection centric
ISO_1	0	0	0	0	17977	3206
ISO_2	0.576	0.546	2.07	1.551	17977	3206
ISO_3	0.721	0.715	0.981	0.764	17977	3206
ANO_1	0.567	0	1.841	0	17977	0
ANO_2	0.738	0	1.291	0	17978	0
ANO_3	0.795	0	1.077	0	17982	0

Phasing MAD set shell

ID	Resolution (Å)	R cullis acentric	R cullis centric	Power acentric	Power centric	Reflection acentric	Reflection centric
ISO_1	7.63-33.86	0	0	0	0	154	153
ISO_1	5.47-7.63	0	0	0	0	318	168
ISO_1	4.48-5.47	0	0	0	0	440	167
ISO_1	3.89-4.48	0	0	0	0	535	166
ISO_1	3.49-3.89	0	0	0	0	618	169
ISO_1	3.19-3.49	0	0	0	0	684	168
ISO_1	2.95-3.19	0	0	0	0	762	163
ISO_1	2.76-2.95	0	0	0	0	814	160
ISO_1	2.6-2.76	0	0	0	0	871	155
ISO_1	2.47-2.6	0	0	0	0	932	146
ISO_1	2.36-2.47	0	0	0	0	988	149
ISO_1	2.26-2.36	0	0	0	0	1024	139
ISO_1	2.17-2.26	0	0	0	0	1089	152
ISO_1	2.09-2.17	0	0	0	0	1133	161
ISO_1	2.02-2.09	0	0	0	0	1169	164
ISO_1	1.96-2.02	0	0	0	0	1201	141
ISO_1	1.9-1.96	0	0	0	0	1263	179
ISO_1	1.84-1.9	0	0	0	0	1302	167
ISO_1	1.8-1.84	0	0	0	0	1318	169
ISO_1	1.75-1.8	0	0	0	0	1362	170
ANO_1	7.63-33.86	0.484	0	1.901	0	154	0
ANO_1	5.47-7.63	0.485	0	2.238	0	318	0
ANO_1	4.48-5.47	0.505	0	2.08	0	440	0
ANO_1	3.89-4.48	0.58	0	1.681	0	535	0
ANO_1	3.49-3.89	0.565	0	1.811	0	618	0
ANO_1	3.19-3.49	0.517	0	2.017	0	684	0
ANO_1	2.95-3.19	0.51	0	2.187	0	762	0
ANO_1	2.76-2.95	0.483	0	2.259	0	814	0
ANO_1	2.6-2.76	0.499	0	2.319	0	871	0
ANO_1	2.47-2.6	0.506	0	2.188	0	932	0
ANO_1	2.36-2.47	0.518	0	2.068	0	988	0
ANO_1	2.26-2.36	0.528	0	1.983	0	1024	0
ANO_1	2.17-2.26	0.563	0	1.867	0	1089	0
ANO_1	2.09-2.17	0.599	0	1.812	0	1133	0
ANO_1	2.02-2.09	0.623	0	1.568	0	1169	0
ANO_1	1.96-2.02	0.648	0	1.602	0	1201	0
ANO_1	1.9-1.96	0.698	0	1.451	0	1263	0
ANO_1	1.84-1.9	0.746	0	1.278	0	1302	0
ANO_1	1.8-1.84	0.785	0	1.182	0	1318	0
ANO_1	1.75-1.8	0.868	0	1.073	0	1362	0
ISO_2	7.63-33.86	0.583	0.467	2.208	1.741	154	153
ISO_2	5.47-7.63	0.468	0.515	2.963	1.803	318	168
ISO_2	4.48-5.47	0.555	0.521	2.157	1.496	440	167
ISO_2	3.89-4.48	0.616	0.589	1.687	1.575	535	166
ISO_2	3.49-3.89	0.628	0.535	1.76	1.475	618	169
ISO_2	3.19-3.49	0.615	0.571	1.872	1.512	684	168
ISO_2	2.95-3.19	0.574	0.526	2.231	1.978	762	163
ISO_2	2.76-2.95	0.537	0.531	2.494	1.792	814	160
ISO_2	2.6-2.76	0.511	0.507	2.586	1.511	871	155
ISO_2	2.47-2.6	0.52	0.594	2.588	1.61	932	146
ISO_2	2.36-2.47	0.538	0.52	2.595	1.775	988	149
ISO_2	2.26-2.36	0.544	0.549	2.367	1.594	1024	139
ISO_2	2.17-2.26	0.56	0.571	2.232	1.63	1089	152
ISO_2	2.09-2.17	0.564	0.609	2.167	1.442	1133	161
ISO_2	2.02-2.09	0.573	0.57	2.08	1.343	1169	164
ISO_2	1.96-2.02	0.562	0.555	1.977	1.314	1201	141
ISO_2	1.9-1.96	0.589	0.735	1.87	1.147	1263	179
ISO_2	1.84-1.9	0.589	0.668	1.686	1.072	1302	167
ISO_2	1.8-1.84	0.618	0.71	1.487	0.905	1318	169
ISO_2	1.75-1.8	0.672	0.698	1.304	0.843	1362	170
ANO_2	7.63-33.86	0.676	0	1.271	0	154	0
ANO_2	5.47-7.63	0.629	0	1.673	0	318	0
ANO_2	4.48-5.47	0.729	0	1.319	0	440	0
ANO_2	3.89-4.48	0.771	0	1.09	0	535	0
ANO_2	3.49-3.89	0.738	0	1.199	0	618	0
ANO_2	3.19-3.49	0.759	0	1.267	0	684	0
ANO_2	2.95-3.19	0.73	0	1.439	0	762	0
ANO_2	2.76-2.95	0.685	0	1.525	0	814	0
ANO_2	2.6-2.76	0.685	0	1.604	0	871	0
ANO_2	2.47-2.6	0.694	0	1.532	0	932	0
ANO_2	2.36-2.47	0.681	0	1.558	0	988	0
ANO_2	2.26-2.36	0.703	0	1.458	0	1024	0
ANO_2	2.17-2.26	0.727	0	1.289	0	1089	0
ANO_2	2.09-2.17	0.735	0	1.276	0	1133	0
ANO_2	2.02-2.09	0.76	0	1.251	0	1169	0
ANO_2	1.96-2.02	0.765	0	1.182	0	1201	0
ANO_2	1.9-1.96	0.78	0	1.099	0	1263	0
ANO_2	1.84-1.9	0.825	0	1.033	0	1302	0
ANO_2	1.8-1.84	0.847	0	0.956	0	1318	0
ANO_2	1.75-1.8	0.893	0	0.824	0	1363	0
ISO_3	7.63-33.86	0.758	0.7	1.073	0.98	154	153
ISO_3	5.47-7.63	0.694	0.767	1.343	0.911	318	168
ISO_3	4.48-5.47	0.722	0.69	1.083	0.846	440	167
ISO_3	3.89-4.48	0.712	0.687	0.834	0.733	535	166
ISO_3	3.49-3.89	0.72	0.676	0.912	0.711	618	169
ISO_3	3.19-3.49	0.711	0.693	0.925	0.736	684	168
ISO_3	2.95-3.19	0.72	0.705	1.009	0.859	762	163
ISO_3	2.76-2.95	0.725	0.684	1.129	0.789	814	160
ISO_3	2.6-2.76	0.702	0.682	1.204	0.746	871	155
ISO_3	2.47-2.6	0.701	0.675	1.14	0.727	932	146
ISO_3	2.36-2.47	0.7	0.684	1.117	0.715	988	149
ISO_3	2.26-2.36	0.704	0.766	1.093	0.713	1024	139
ISO_3	2.17-2.26	0.707	0.732	0.997	0.776	1089	152
ISO_3	2.09-2.17	0.706	0.764	0.963	0.591	1133	161
ISO_3	2.02-2.09	0.716	0.757	0.942	0.68	1169	164
ISO_3	1.96-2.02	0.722	0.747	0.921	0.587	1201	141
ISO_3	1.9-1.96	0.728	0.855	0.856	0.564	1263	179
ISO_3	1.84-1.9	0.751	0.854	0.782	0.528	1302	167
ISO_3	1.8-1.84	0.766	0.789	0.687	0.422	1318	169
ISO_3	1.75-1.8	0.803	0.847	0.617	0.426	1362	170
ANO_3	7.63-33.86	0.743	0	1.215	0	154	0
ANO_3	5.47-7.63	0.652	0	1.568	0	318	0
ANO_3	4.48-5.47	0.767	0	1.136	0	440	0
ANO_3	3.89-4.48	0.835	0	0.978	0	535	0
ANO_3	3.49-3.89	0.834	0	0.96	0	618	0
ANO_3	3.19-3.49	0.784	0	1.107	0	684	0
ANO_3	2.95-3.19	0.771	0	1.189	0	762	0
ANO_3	2.76-2.95	0.74	0	1.328	0	814	0
ANO_3	2.6-2.76	0.722	0	1.393	0	871	0
ANO_3	2.47-2.6	0.739	0	1.25	0	932	0
ANO_3	2.36-2.47	0.74	0	1.277	0	988	0
ANO_3	2.26-2.36	0.75	0	1.233	0	1024	0
ANO_3	2.17-2.26	0.794	0	1.067	0	1089	0
ANO_3	2.09-2.17	0.803	0	1.018	0	1133	0
ANO_3	2.02-2.09	0.826	0	0.947	0	1169	0
ANO_3	1.96-2.02	0.83	0	0.945	0	1201	0
ANO_3	1.9-1.96	0.843	0	0.867	0	1263	0
ANO_3	1.84-1.9	0.877	0	0.793	0	1302	0
ANO_3	1.8-1.84	0.897	0	0.688	0	1318	0
ANO_3	1.75-1.8	0.927	0	0.631	0	1367	0

Phasing MAD set site

ID	Cartn x (Å)	Cartn y (Å)	Cartn z (Å)	Atom type symbol	B iso	Occupancy
1	-2.115	-11.338	-16.82	SE	15.89	1.71
2	-3.77	-15.079	-53.632	SE	19.59	1.47
3	-4.463	-45.126	-78.563	SE	29.9	0.95

Phasing dm

Method: Solvent flattening and Histogram matching / Reflection: 21466

Phasing dm shell

Resolution (Å)	Delta phi final	FOM	Reflection
6.47-100	47.1	0.913	503
5.05-6.47	35.6	0.955	510
4.39-5.05	40.2	0.962	508
3.96-4.39	39.8	0.959	510
3.66-3.96	42.5	0.959	520
3.41-3.66	42.9	0.959	549
3.21-3.41	39.7	0.955	590
3.04-3.21	43.4	0.94	639
2.9-3.04	42	0.94	648
2.77-2.9	43	0.932	683
2.66-2.77	38.9	0.933	722
2.56-2.66	40.2	0.935	730
2.47-2.56	39.2	0.924	754
2.39-2.47	43	0.927	781
2.32-2.39	42.1	0.918	819
2.25-2.32	39.9	0.922	831
2.19-2.25	39.7	0.916	840
2.14-2.19	41.1	0.902	878
2.08-2.14	44	0.904	912
2.03-2.08	42.7	0.894	899
1.99-2.03	42	0.899	933
1.95-1.99	45.9	0.891	969
1.91-1.95	46.8	0.878	964
1.87-1.91	47.8	0.865	999
1.83-1.87	53.1	0.861	1020
1.8-1.83	53.6	0.824	1014
1.75-1.8	59.3	0.775	1741

-
Processing

Software

Name	Version	Classification
DENZO		data reduction
SCALEPACK		data scaling
SHARP		phasing
DM	5	phasing
REFMAC	refmac_5.2.0005	refinement
PDB_EXTRACT	1.7	data extraction

Refinement

Method to determine structure:

MAD / Resolution: 1.75→33.86 Å / Cor.coef. F_o:F_c: 0.954 / Cor.coef. F_o:F_c free: 0.943 / SU B: 2.025 / SU ML: 0.067 / Cross valid method: THROUGHOUT / ESU R: 0.117 / ESU R Free: 0.113 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS, SELENIUM C COEFFICIENT FOR STRUCTURE FACTOR CALCULATION SET TO -9.00, MOLPROBITY USED TO ASSIST IN FINAL MODEL BUILDING.

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.21555	1101	5.1 %	RANDOM
R_work	0.17885	-	-	-
obs	0.18071	20362	100 %	-

Solvent computation

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

Displacement parameters

B_iso mean: 19.118 Å²

	B_aniso -1	B_aniso -2
1-	0 Å²	0 Å²
2-	-	0 Å²
3-	-	-

Refinement step

Cycle: LAST / Resolution: 1.75→33.86 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	1585	0	5	188	1778

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.02	0.021	1641
X-RAY DIFFRACTION	r_bond_other_d
X-RAY DIFFRACTION	r_angle_refined_deg	1.764	1.938	2238
X-RAY DIFFRACTION	r_angle_other_deg
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.338	5	211
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	36.991	23.933	89
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	13.481	15	291
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	19.865	15	12
X-RAY DIFFRACTION	r_chiral_restr	0.152	0.2	238
X-RAY DIFFRACTION	r_gen_planes_refined	0.009	0.02	1285
X-RAY DIFFRACTION	r_gen_planes_other
X-RAY DIFFRACTION	r_nbd_refined	0.215	0.2	724
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined	0.309	0.2	1089
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.161	0.2	170
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	0.179	0.2	33
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.116	0.2	14
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	1.4	1.5	1007
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it	2.019	2	1576
X-RAY DIFFRACTION	r_scbond_it	2.971	3	724
X-RAY DIFFRACTION	r_scangle_it	4.429	4.5	649
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

LS refinement shell

Resolution: 1.75→1.795 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.299	60	-
R_work	0.195	1483	-
obs	-	-	99.94 %

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