3E5L

Crystal structure of CYP105P1 H72A mutant


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP82984.2M sodium formate, pH8.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
4.2470.98

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 88.635α = 90
b = 88.635β = 90
c = 191.473γ = 90
Symmetry
Space GroupP 43 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 42008-05-31MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPHOTON FACTORY BEAMLINE BL-6A1.0000Photon FactoryBL-6A

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
12.45099.80.0648.313.33077753.116
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)
12.42.491000.4725.312.7

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 3E5J2.440.2329066153999.740.186560.184010.23533RANDOM41.172
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]
0.080.08-0.15
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.755
r_dihedral_angle_4_deg20.444
r_dihedral_angle_3_deg19.03
r_dihedral_angle_1_deg7.692
r_scangle_it5.233
r_scbond_it3.317
r_angle_refined_deg2.186
r_mcangle_it1.994
r_mcbond_it1.262
r_nbtor_refined0.318
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.755
r_dihedral_angle_4_deg20.444
r_dihedral_angle_3_deg19.03
r_dihedral_angle_1_deg7.692
r_scangle_it5.233
r_scbond_it3.317
r_angle_refined_deg2.186
r_mcangle_it1.994
r_mcbond_it1.262
r_nbtor_refined0.318
r_nbd_refined0.232
r_symmetry_vdw_refined0.229
r_xyhbond_nbd_refined0.156
r_chiral_restr0.151
r_symmetry_hbond_refined0.123
r_bond_refined_d0.023
r_gen_planes_refined0.009
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 Atoms3046
Nucleic Acid Atoms
Solvent Atoms225
Heterogen Atoms43

Software

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