3A4G

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


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1JINPDB ENTRY 1JIN

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.529338% PEG400, 0.1M Bis-tris, pH7.5, 50mM CaCl2, 60mM NaCl, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.3848.43

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 61.675α = 90
b = 61.675β = 90
c = 98.799γ = 120
Symmetry
Space GroupP 31

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315r2006-05-19MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPHOTON FACTORY BEAMLINE BL-5A1.0000Photon FactoryBL-5A

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
11.755099.30.07521.95.3420124201223.2
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)
1.751.8193.20.3163.73.23957

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 1JIN1.7529.443990120721000.187480.185010.23624RANDOM28.704
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]
0.610.30.61-0.91
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.432
r_dihedral_angle_4_deg19.194
r_dihedral_angle_3_deg14.91
r_dihedral_angle_1_deg6.017
r_scangle_it3.882
r_scbond_it2.487
r_mcangle_it1.783
r_angle_refined_deg1.531
r_mcbond_it1.088
r_nbtor_refined0.304
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.432
r_dihedral_angle_4_deg19.194
r_dihedral_angle_3_deg14.91
r_dihedral_angle_1_deg6.017
r_scangle_it3.882
r_scbond_it2.487
r_mcangle_it1.783
r_angle_refined_deg1.531
r_mcbond_it1.088
r_nbtor_refined0.304
r_symmetry_vdw_refined0.272
r_nbd_refined0.213
r_xyhbond_nbd_refined0.16
r_symmetry_hbond_refined0.118
r_chiral_restr0.099
r_bond_refined_d0.015
r_gen_planes_refined0.006
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3062
Nucleic Acid Atoms
Solvent Atoms338
Heterogen Atoms51

Software

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