3CV8 | pdb_00003cv8

Crystal structure of vitamin D hydroxylase cytochrome P450 105A1 (R84F mutant)


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2ZBZPDB ENTRY 2ZBZ

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.128316% PEGMME 2000, 10% MPD, 0.1M Bis-tris, 0.2M sodium chloride, pH 6.1, VAPOR DIFFUSION, SITTING DROP, temperature 283K
Crystal Properties
Matthews coefficientSolvent content
2.1643.07

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 52.5α = 90
b = 53.384β = 90
c = 138.97γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray90CCDADSC QUANTUM 210mirrors2007-06-18MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSPRING-8 BEAMLINE BL44B21.00SPring-8BL44B2

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
122099.40.07323.15.327037-317.7
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
22.0798.20.1918.35.42617

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (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 DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 2ZBZ22025633137899.340.183560.181120.180.229920.23RANDOM18.306
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]
0.66-1.050.39
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.887
r_dihedral_angle_4_deg15.994
r_dihedral_angle_3_deg12.796
r_dihedral_angle_1_deg5.473
r_scangle_it2.972
r_scbond_it1.849
r_angle_refined_deg1.271
r_mcangle_it1.189
r_mcbond_it0.71
r_nbtor_refined0.3
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.887
r_dihedral_angle_4_deg15.994
r_dihedral_angle_3_deg12.796
r_dihedral_angle_1_deg5.473
r_scangle_it2.972
r_scbond_it1.849
r_angle_refined_deg1.271
r_mcangle_it1.189
r_mcbond_it0.71
r_nbtor_refined0.3
r_symmetry_vdw_refined0.202
r_nbd_refined0.197
r_xyhbond_nbd_refined0.168
r_symmetry_hbond_refined0.154
r_chiral_restr0.089
r_bond_refined_d0.011
r_gen_planes_refined0.005
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 AtomsNumber
Protein Atoms3107
Nucleic Acid Atoms
Solvent Atoms346
Heterogen Atoms43

Software

Software
Software NamePurpose
REFMACrefinement
BSSdata collection
HKL-2000data reduction
HKL-2000data scaling
REFMACphasing