6GMF

Structure of Cytochrome P450 CYP109Q5 from Chondromyces apiculatus


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP8.52980.1 M Tris-HCl pH 8.5, 28% (w/v) PEG 3350, 0.1 M NaCl
Crystal Properties
Matthews coefficientSolvent content
2.1342

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 44.69α = 90
b = 55.02β = 91.67
c = 74.8γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray120PIXELDECTRIS PILATUS 6M-F2017-12-17MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I040.97950DiamondI04

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rpim I (All)CC (Half)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
11.5555.0299.80.050.04111.63.952220
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.551.5899.80.530.450.8224

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 REPLACEMENTTHROUGHOUT5OFQ1.5544.7149666252998.890.186690.184940.2195RANDOM24.768
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]
-1.76-0.36-1.132.9
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg25.073
r_dihedral_angle_4_deg19.531
r_dihedral_angle_3_deg14.452
r_dihedral_angle_1_deg5.953
r_long_range_B_refined4.942
r_long_range_B_other4.899
r_scangle_other3.804
r_mcangle_it2.735
r_mcangle_other2.735
r_scbond_other2.661
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg25.073
r_dihedral_angle_4_deg19.531
r_dihedral_angle_3_deg14.452
r_dihedral_angle_1_deg5.953
r_long_range_B_refined4.942
r_long_range_B_other4.899
r_scangle_other3.804
r_mcangle_it2.735
r_mcangle_other2.735
r_scbond_other2.661
r_scbond_it2.659
r_mcbond_it1.98
r_mcbond_other1.971
r_angle_refined_deg1.589
r_angle_other_deg1.076
r_chiral_restr0.086
r_bond_refined_d0.012
r_gen_planes_refined0.009
r_gen_planes_other0.006
r_bond_other_d0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2932
Nucleic Acid Atoms
Solvent Atoms255
Heterogen Atoms43

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing