8Q6Y

Crystal structure of Cytochrome P450 GymB5 from Streptomyces katrae in complex with cYY and Hypoxanthine


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1N40 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP27720 mM sodium formate, 20 mM ammonium acetate, 20 mM sodium citrate, 20 mM potassium sodium tartrate, 20 mM sodium oxamate, 13% MPD, 13% PEG 1000, 13% PEG3350, 100 mM BIS-Tris pH 8.7, 1.25% DMSO
Crystal Properties
Matthews coefficientSolvent content
2.5952.51

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 64.83α = 90
b = 95.482β = 108.28
c = 79.451γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 16M2023-03-30MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X06SA1SLSX06SA

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)Rrim 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
11.849.0299.80.130.9910.3583878
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.811.920.64

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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 REPLACEMENTTHROUGHOUT1.8141.7282200167899.850.185570.184940.21633RANDOM30.883
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]
0.37-0.47-1.771.4
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg28.024
r_dihedral_angle_4_deg18.213
r_dihedral_angle_3_deg13.914
r_long_range_B_refined7.165
r_long_range_B_other7.137
r_dihedral_angle_1_deg6.288
r_scangle_other3.411
r_scbond_other2.467
r_scbond_it2.466
r_mcangle_it2.023
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg28.024
r_dihedral_angle_4_deg18.213
r_dihedral_angle_3_deg13.914
r_long_range_B_refined7.165
r_long_range_B_other7.137
r_dihedral_angle_1_deg6.288
r_scangle_other3.411
r_scbond_other2.467
r_scbond_it2.466
r_mcangle_it2.023
r_mcangle_other2.023
r_angle_refined_deg1.704
r_angle_other_deg1.43
r_mcbond_it1.3
r_mcbond_other1.299
r_chiral_restr0.088
r_bond_refined_d0.011
r_gen_planes_refined0.01
r_gen_planes_other0.003
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 Atoms5922
Nucleic Acid Atoms
Solvent Atoms554
Heterogen Atoms152

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing