2ZBY

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


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.627720% 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 coefficientSolvent content
2.2545.31

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 53.437α = 90
b = 53.586β = 90
c = 141.339γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray90CCDADSC QUANTUM 210mirrors2007-05-19MSINGLE 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
11.62099.40.00426.57.954213-330.3
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)
1.61.6696.50.32956.55192

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 2ZBX1.619.835139551395272699.430.197410.197410.196150.22154RANDOM24.184
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
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.764
r_dihedral_angle_4_deg16.679
r_dihedral_angle_3_deg12.635
r_dihedral_angle_1_deg5.123
r_scangle_it2.637
r_scbond_it1.679
r_angle_refined_deg1.22
r_mcangle_it1.113
r_mcbond_it0.673
r_nbtor_refined0.302
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.764
r_dihedral_angle_4_deg16.679
r_dihedral_angle_3_deg12.635
r_dihedral_angle_1_deg5.123
r_scangle_it2.637
r_scbond_it1.679
r_angle_refined_deg1.22
r_mcangle_it1.113
r_mcbond_it0.673
r_nbtor_refined0.302
r_nbd_refined0.197
r_symmetry_vdw_refined0.191
r_symmetry_hbond_refined0.149
r_xyhbond_nbd_refined0.116
r_chiral_restr0.082
r_bond_refined_d0.009
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 Atoms3068
Nucleic Acid Atoms
Solvent Atoms454
Heterogen Atoms43

Software

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