2ZBX | pdb_00002zbx

Crystal structure of vitamin D hydroxylase cytochrome P450 105A1 (wild type) with imidazole bound

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	Other		Starting model was obtained by MAD phasing using iron atom as a anomalous scatterer

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.2	283	24% PEG 8000, 0.1M imidazole, 0.2M sodium chloride, 0.2M sodium formate, pH 6.2, VAPOR DIFFUSION, SITTING DROP, temperature 283K

Crystal Properties
Matthews coefficient	Solvent content
2.21	44.32

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 52.575	α = 90
b = 53.754	β = 90
c = 140.948	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	90	CCD	ADSC QUANTUM 210	mirrors	2006-09-23	M	SINGLE WAVELENGTH
2	1	x-ray	90	CCD	ADSC QUANTUM 210	mirrors	2005-10-20	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SPRING-8 BEAMLINE BL44B2	1.0000	SPring-8	BL44B2
2	SYNCHROTRON	SPRING-8 BEAMLINE BL44B2	1.7377, 1.7403, 1.7310, 1.7240	SPring-8	BL44B2

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
1,2	1.5	20	97.1	0.035	32.3	9		62925		-3	25.7

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	1.5	1.53	91.1		0.264	7.4	8.1	2863

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	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	MAD and MOLECULAR REPLACEMENT	THROUGHOUT	Starting model was obtained by MAD phasing using iron atom as a anomalous scatterer	1.5	19.62	59532	59532	3180	96.82	0.19578	0.19578	0.19434	0.19	0.22327	0.22	RANDOM	18.555

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]
0.7			-0.61		-0.09

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.441
r_dihedral_angle_4_deg	15.114
r_dihedral_angle_3_deg	12.269
r_dihedral_angle_1_deg	4.865
r_scangle_it	2.788
r_scbond_it	1.852
r_angle_refined_deg	1.254
r_mcangle_it	1.167
r_mcbond_it	0.739
r_nbtor_refined	0.304

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.441
r_dihedral_angle_4_deg	15.114
r_dihedral_angle_3_deg	12.269
r_dihedral_angle_1_deg	4.865
r_scangle_it	2.788
r_scbond_it	1.852
r_angle_refined_deg	1.254
r_mcangle_it	1.167
r_mcbond_it	0.739
r_nbtor_refined	0.304
r_nbd_refined	0.2
r_symmetry_vdw_refined	0.123
r_xyhbond_nbd_refined	0.12
r_symmetry_hbond_refined	0.12
r_chiral_restr	0.084
r_bond_refined_d	0.009
r_gen_planes_refined	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3072
Nucleic Acid Atoms
Solvent Atoms	524
Heterogen Atoms	48

Software

Software
Software Name	Purpose
REFMAC	refinement
BSS	data collection
HKL-2000	data reduction
HKL-2000	data scaling
SHARP	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.