8Q6X

Crystal structure of Cytochrome P450 GymB5 from Streptomyces katrae


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 tartate, 20 mM sodium oxamate, 13% MPD, 13% PEG 1000, 13% PEG3350, 100 mM BIS-Tris pH 8.7
Crystal Properties
Matthews coefficientSolvent content
2.5752.23

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 63.166α = 90
b = 95.544β = 109.22
c = 81.459γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 16M2023-02-11MSINGLE 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
11.949.0299.80.120.9910.94.879072
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)
11.912.020.57

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-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT1.9149.0268841213099.850.170960.169810.180.208180.21RANDOM32.3
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]
2.5-1.03-1.57-0.17
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg27.945
r_dihedral_angle_4_deg17.52
r_dihedral_angle_3_deg15.452
r_long_range_B_refined6.429
r_long_range_B_other6.401
r_dihedral_angle_1_deg6.058
r_scangle_other5.452
r_scbond_other3.58
r_scbond_it3.579
r_mcangle_it3.512
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5888
Nucleic Acid Atoms
Solvent Atoms505
Heterogen Atoms86

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing