3CV9

Crystal structure of vitamin D hydroxylase cytochrome P450 105A1 (R73A/R84A mutant) in complex with 1alpha,25-dihydroxyvitamin D3


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.228326% PEGMME 2000, 0.1M Bis-tris, 0.2M sodium chlorife, pH 6.2, VAPOR DIFFUSION, SITTING DROP, temperature 283K
Crystal Properties
Matthews coefficientSolvent content
2.2445.07

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 53.315α = 90
b = 53.659β = 90
c = 140.605γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray90CCDADSC QUANTUM 210mirrors2007-06-28MSINGLE 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 Sym 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
11.72098.50.0428.87.14513945139-321.6
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)
1.71.7687.10.3375.15.33913

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-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 2ZBZ1.72042422226698.780.201770.199070.25347RANDOM23.075
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]
1.18-1.450.27
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.629
r_dihedral_angle_4_deg18.279
r_dihedral_angle_3_deg13.304
r_dihedral_angle_1_deg5.634
r_scangle_it2.994
r_scbond_it2.094
r_angle_refined_deg1.554
r_mcangle_it1.316
r_mcbond_it0.849
r_nbtor_refined0.307
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.629
r_dihedral_angle_4_deg18.279
r_dihedral_angle_3_deg13.304
r_dihedral_angle_1_deg5.634
r_scangle_it2.994
r_scbond_it2.094
r_angle_refined_deg1.554
r_mcangle_it1.316
r_mcbond_it0.849
r_nbtor_refined0.307
r_nbd_refined0.212
r_symmetry_hbond_refined0.181
r_xyhbond_nbd_refined0.169
r_symmetry_vdw_refined0.152
r_chiral_restr0.108
r_bond_refined_d0.014
r_gen_planes_refined0.007
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3150
Nucleic Acid Atoms
Solvent Atoms463
Heterogen Atoms73

Software

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