3A4G | pdb_00003a4g

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

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1JIN	PDB ENTRY 1JIN

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.5	293	38% PEG400, 0.1M Bis-tris, pH7.5, 50mM CaCl2, 60mM NaCl, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.38	48.43

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 61.675	α = 90
b = 61.675	β = 90
c = 98.799	γ = 120

Symmetry
Space Group	P 31

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		2006-05-19	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PHOTON FACTORY BEAMLINE BL-5A	1.0000	Photon Factory	BL-5A

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	1.75	50	99.3	0.075	21.9	5.3	42012	42012			23.2

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)
	1.75	1.81	93.2		0.316	3.7	3.2	3957

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 1JIN	1.75	29.44	39901	2072	100	0.18748	0.18501	0.19	0.23624	0.18	RANDOM	28.704

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]
0.61	0.3		0.61		-0.91

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.432
r_dihedral_angle_4_deg	19.194
r_dihedral_angle_3_deg	14.91
r_dihedral_angle_1_deg	6.017
r_scangle_it	3.882
r_scbond_it	2.487
r_mcangle_it	1.783
r_angle_refined_deg	1.531
r_mcbond_it	1.088
r_nbtor_refined	0.304

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.432
r_dihedral_angle_4_deg	19.194
r_dihedral_angle_3_deg	14.91
r_dihedral_angle_1_deg	6.017
r_scangle_it	3.882
r_scbond_it	2.487
r_mcangle_it	1.783
r_angle_refined_deg	1.531
r_mcbond_it	1.088
r_nbtor_refined	0.304
r_symmetry_vdw_refined	0.272
r_nbd_refined	0.213
r_xyhbond_nbd_refined	0.16
r_symmetry_hbond_refined	0.118
r_chiral_restr	0.099
r_bond_refined_d	0.015
r_gen_planes_refined	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3062
Nucleic Acid Atoms
Solvent Atoms	338
Heterogen Atoms	51

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.