2ZBY | pdb_00002zby

Crystal structure of vitamin D hydroxylase cytochrome P450 105A1 (R84A mutant)

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.6	277	20% PEG 8000, 0.1M bis-Tris-propane, 0.2M sodium chloride, 50mM lithium nitrate, pH 6.6, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.25	45.31

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 53.437	α = 90
b = 53.586	β = 90
c = 141.339	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	2007-05-19	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SPRING-8 BEAMLINE BL44B2	1.00	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	1.6	20	99.4	0.004	26.5	7.9		54213		-3	30.3

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)
	1.6	1.66	96.5		0.329	5	6.5	5192

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	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 2ZBX	1.6	19.83	51395	51395	2726	99.43	0.19741	0.19741	0.19615	0.2	0.22154	0.22	RANDOM	24.184

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]
0.94			-0.69		-0.25

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.764
r_dihedral_angle_4_deg	16.679
r_dihedral_angle_3_deg	12.635
r_dihedral_angle_1_deg	5.123
r_scangle_it	2.637
r_scbond_it	1.679
r_angle_refined_deg	1.22
r_mcangle_it	1.113
r_mcbond_it	0.673
r_nbtor_refined	0.302
r_nbd_refined	0.197
r_symmetry_vdw_refined	0.191
r_symmetry_hbond_refined	0.149
r_xyhbond_nbd_refined	0.116
r_chiral_restr	0.082
r_bond_refined_d	0.009
r_gen_planes_refined	0.005
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3068
Nucleic Acid Atoms
Solvent Atoms	454
Heterogen Atoms	43

Software

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