3E5K

Crystal structure of CYP105P1 wild-type 4-phenylimidazole complex


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3E5JPDB ENTRY 3E5J

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP82983.8M sodium formate, pH8.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
4.7674.17

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 143.725α = 90
b = 143.725β = 90
c = 70.943γ = 120
Symmetry
Space GroupP 31 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 2102007-02-07MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPHOTON FACTORY BEAMLINE AR-NW12A1.0000Photon FactoryAR-NW12A

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
12.6501000.06938.711.22630058.711
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)
12.62.691000.4294.311.1

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 3E5J2.634.522492813311000.178570.175650.23553RANDOM39.991
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]
-0.04-0.02-0.040.05
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.41
r_dihedral_angle_4_deg26.239
r_dihedral_angle_3_deg23.156
r_dihedral_angle_1_deg9.383
r_scangle_it8.32
r_scbond_it5.716
r_angle_refined_deg3.549
r_mcangle_it3.467
r_mcbond_it2.126
r_nbtor_refined0.357
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.41
r_dihedral_angle_4_deg26.239
r_dihedral_angle_3_deg23.156
r_dihedral_angle_1_deg9.383
r_scangle_it8.32
r_scbond_it5.716
r_angle_refined_deg3.549
r_mcangle_it3.467
r_mcbond_it2.126
r_nbtor_refined0.357
r_nbd_refined0.286
r_symmetry_vdw_refined0.275
r_symmetry_hbond_refined0.257
r_chiral_restr0.231
r_xyhbond_nbd_refined0.172
r_metal_ion_refined0.087
r_bond_refined_d0.017
r_gen_planes_refined0.016
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_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 Atoms2967
Nucleic Acid Atoms
Solvent Atoms127
Heterogen Atoms54

Software

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