5JRA

Nitric oxide complex of the L16V mutant of cytochrome c prime from Alcaligenes xylosoxidans

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2YLI

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.5	294	2.2M Ammonium sulfate 0.1 M HEPES pH 7.5

Crystal Properties
Matthews coefficient	Solvent content
2.74	55.04

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 53.199	α = 90
b = 53.199	β = 90
c = 180.679	γ = 120

Symmetry
Space Group	P 65 2 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	PIXEL	DECTRIS PILATUS 6M-F		2012-10-03	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X10SA	1.0	SLS	X10SA

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Sym I (Observed)	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	1.38	46.072	100	0.051	15.4	7.6		32339

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.38	1.45	100		0.744	1	6.8

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	2YLI	1.38	46.07	30600	1633	99.98	0.1637	0.1626	0.1858	RANDOM	24.331

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]
-0.21	-0.1		-0.21		0.67

RMS Deviations
Key	Refinement Restraint Deviation
r_sphericity_free	37.824
r_dihedral_angle_2_deg	34.924
r_dihedral_angle_4_deg	22.861
r_dihedral_angle_3_deg	15.546
r_sphericity_bonded	13.661
r_dihedral_angle_1_deg	5.105
r_rigid_bond_restr	3.659
r_mcangle_it	3.485
r_mcbond_it	2.805
r_mcbond_other	2.725

RMS Deviations
Key	Refinement Restraint Deviation
r_sphericity_free	37.824
r_dihedral_angle_2_deg	34.924
r_dihedral_angle_4_deg	22.861
r_dihedral_angle_3_deg	15.546
r_sphericity_bonded	13.661
r_dihedral_angle_1_deg	5.105
r_rigid_bond_restr	3.659
r_mcangle_it	3.485
r_mcbond_it	2.805
r_mcbond_other	2.725
r_angle_refined_deg	2.366
r_angle_other_deg	1.851
r_chiral_restr	0.116
r_bond_refined_d	0.017
r_gen_planes_refined	0.009
r_gen_planes_other	0.007
r_bond_other_d	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	948
Nucleic Acid Atoms
Solvent Atoms	139
Heterogen Atoms	70

Software

Software
Software Name	Purpose
SCALA	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
PHASER	phasing

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.