4WWB

High-resolution structure of the Ni-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, sodium/potassium phosphate

Crystal Properties
Matthews coefficient	Solvent content
1.93	36.2

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 32.401	α = 90
b = 32.401	β = 90
c = 195.331	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 Sym I (Observed)	Rrim I (All)	Rpim 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	1.107	39.066	98.9	0.089	0.103	0.036	16.6	8.4	42671	42671

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Rpim I (All)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.11	1.17	96.4		0.333	0.333	0.13	2.2	8.1	5927

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	2Y39	1.11	30	40322	1980	98.8	0.109	0.1083	0.1237	RANDOM	8.822

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]
-0.02			-0.02		0.04

RMS Deviations
Key	Refinement Restraint Deviation
r_sphericity_free	25.873
r_dihedral_angle_2_deg	25.767
r_dihedral_angle_4_deg	20.283
r_dihedral_angle_3_deg	11.916
r_sphericity_bonded	9.474
r_dihedral_angle_1_deg	4.28
r_rigid_bond_restr	2.926
r_angle_refined_deg	1.678
r_mcangle_it	1.377
r_mcbond_it	1.155

RMS Deviations
Key	Refinement Restraint Deviation
r_sphericity_free	25.873
r_dihedral_angle_2_deg	25.767
r_dihedral_angle_4_deg	20.283
r_dihedral_angle_3_deg	11.916
r_sphericity_bonded	9.474
r_dihedral_angle_1_deg	4.28
r_rigid_bond_restr	2.926
r_angle_refined_deg	1.678
r_mcangle_it	1.377
r_mcbond_it	1.155
r_mcbond_other	1.155
r_angle_other_deg	0.794
r_chiral_restr	0.088
r_bond_refined_d	0.013
r_gen_planes_refined	0.008
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	887
Nucleic Acid Atoms
Solvent Atoms	260
Heterogen Atoms	11

Software

Software
Software Name	Purpose
REFMAC	refinement
SCALA	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 R01GM133198.