3A4H

Structure of cytochrome P450 vdh from Pseudonocardia autotrophica (orthorhombic crystal form)

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3A4G	PDB ENTRY 3A4G

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.5	293	26% PEG1000, 0.1M Bis-tris, pH7.5, 50mM CaCl2, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.35	47.7

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 63.595	α = 90
b = 65.793	β = 90
c = 102.264	γ = 90

Symmetry
Space Group	P 21 21 21

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 4r		2006-12-22	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PHOTON FACTORY BEAMLINE BL-17A	1.0000	Photon Factory	BL-17A

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge 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	3.05	50	97.6	0.09	18.9	3.6	8366	8366			45

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)
	3.05	3.16	97.9		0.317	6	3.8	822

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	PDB ENTRY 3A4G	3.06	45.74	7852	430	97.01	0.21952	0.21672	0.26978	RANDOM	44.138

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]
-3.82			7.4		-3.58

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.869
r_dihedral_angle_3_deg	16.494
r_dihedral_angle_4_deg	14.375
r_dihedral_angle_1_deg	4.343
r_angle_refined_deg	0.96
r_scangle_it	0.813
r_mcangle_it	0.585
r_scbond_it	0.46
r_mcbond_it	0.323
r_nbtor_refined	0.295

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.869
r_dihedral_angle_3_deg	16.494
r_dihedral_angle_4_deg	14.375
r_dihedral_angle_1_deg	4.343
r_angle_refined_deg	0.96
r_scangle_it	0.813
r_mcangle_it	0.585
r_scbond_it	0.46
r_mcbond_it	0.323
r_nbtor_refined	0.295
r_symmetry_vdw_refined	0.181
r_nbd_refined	0.18
r_symmetry_hbond_refined	0.155
r_xyhbond_nbd_refined	0.116
r_chiral_restr	0.062
r_bond_refined_d	0.006
r_gen_planes_refined	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3094
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms	44

Software

Software
Software Name	Purpose
ADSC	data collection
AMoRE	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

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.