4WWD | pdb_00004wwd

High-resolution structure of the Co-bound form of the Y135F mutant of C. metallidurans CnrXs

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.5	298	PEG 3350, HEPES, NaH2P04/KH2PO4

Crystal Properties
Matthews coefficient	Solvent content
1.94	36.52

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 32.42	α = 90
b = 32.42	β = 90
c = 196.1	γ = 90

Symmetry
Space Group	P 41 21 2

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	CCD	ADSC QUANTUM 315r		2013-05-13	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE BM30A	0.979725	ESRF	BM30A

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Net I Over Average Sigma (I)	Redundancy	Number Reflections (All)	Number Reflections (Observed)	Observed Criterion Sigma (F)	Observed Criterion Sigma (I)	B (Isotropic) From Wilson Plot
1	1.11	20	99.2	0.103	0.11	12.29	7.9		78323		-3	11.253

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.11	1.18	95.6		0.596	0.639	3.77

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	1.3	19.79	40322	1430	99.87	0.1326	0.1304	0.13	0.1716	0.17	RANDOM	12.327

Temperature Factor Modeling
Anisotropic B[1][1]	Anisotropic B[1][2]	Anisotropic B[1][3]	Anisotropic B[2][2]	Anisotropic B[2][3]	Anisotropic B[3][3]
-0.06			-0.06		0.13

RMS Deviations
Key	Refinement Restraint Deviation
r_sphericity_free	36.251
r_dihedral_angle_2_deg	26.229
r_dihedral_angle_4_deg	19.191
r_dihedral_angle_3_deg	12.432
r_sphericity_bonded	10.676
r_dihedral_angle_1_deg	4.137
r_rigid_bond_restr	1.966
r_mcangle_it	1.739
r_mcbond_it	1.484
r_mcbond_other	1.483

RMS Deviations
Key	Refinement Restraint Deviation
r_sphericity_free	36.251
r_dihedral_angle_2_deg	26.229
r_dihedral_angle_4_deg	19.191
r_dihedral_angle_3_deg	12.432
r_sphericity_bonded	10.676
r_dihedral_angle_1_deg	4.137
r_rigid_bond_restr	1.966
r_mcangle_it	1.739
r_mcbond_it	1.484
r_mcbond_other	1.483
r_angle_refined_deg	1.457
r_angle_other_deg	0.853
r_chiral_restr	0.086
r_bond_refined_d	0.011
r_gen_planes_refined	0.007
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	882
Nucleic Acid Atoms
Solvent Atoms	260
Heterogen Atoms	12

Software

Software
Software Name	Purpose
REFMAC	refinement
XSCALE	data scaling
PDB_EXTRACT	data extraction

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.