3A4H

Structure of cytochrome P450 vdh from Pseudonocardia autotrophica (orthorhombic crystal form)


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3A4GPDB ENTRY 3A4G

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.529326% PEG1000, 0.1M Bis-tris, pH7.5, 50mM CaCl2, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.3547.7

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 63.595α = 90
b = 65.793β = 90
c = 102.264γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 4r2006-12-22MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPHOTON FACTORY BEAMLINE BL-17A1.0000Photon FactoryBL-17A

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
13.055097.60.0918.93.68366836645
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
3.053.1697.90.31763.8822

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 3A4G3.0645.74785243097.010.219520.216720.26978RANDOM44.138
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]
-3.827.4-3.58
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.869
r_dihedral_angle_3_deg16.494
r_dihedral_angle_4_deg14.375
r_dihedral_angle_1_deg4.343
r_angle_refined_deg0.96
r_scangle_it0.813
r_mcangle_it0.585
r_scbond_it0.46
r_mcbond_it0.323
r_nbtor_refined0.295
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.869
r_dihedral_angle_3_deg16.494
r_dihedral_angle_4_deg14.375
r_dihedral_angle_1_deg4.343
r_angle_refined_deg0.96
r_scangle_it0.813
r_mcangle_it0.585
r_scbond_it0.46
r_mcbond_it0.323
r_nbtor_refined0.295
r_symmetry_vdw_refined0.181
r_nbd_refined0.18
r_symmetry_hbond_refined0.155
r_xyhbond_nbd_refined0.116
r_chiral_restr0.062
r_bond_refined_d0.006
r_gen_planes_refined0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3094
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms44

Software

Software
Software NamePurpose
ADSCdata collection
AMoREphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling