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Cytochrome P450 158A2 (CYP158A2) variant P354L bound to substrate flaviolin
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1SE6
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 298 The protein sample had a concentration of 20 mg/mL in 20 mM Tris pH 7.4 and 2 mM flaviolin. The well solution was 0.1 M Bis-Tris pH 7.0 and 25% PEG 3350. Crystallization occurred by vapor diffusion in a hanging drop of 1:1, protein:well
Crystal Properties Matthews coefficient Solvent content 2.26 45.55
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 56.3 α = 90 b = 70.349 β = 90 c = 101.352 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL RIGAKU HyPix-3000 2023-03-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU 1.54
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) CC (Half) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 2.2 28.97 99.98 0.998 21.34 11.7 246162 16.19
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.2 2.32 0.96 8.81
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2.2 28.97 1.36 21037 1040 99.98 0.202 0.1996 0.1995 0.2482 0.2483 20.92
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 14.8116 f_angle_d 1.2951 f_chiral_restr 0.0608 f_plane_restr 0.0363 f_bond_d 0.0103
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3056 Nucleic Acid Atoms Solvent Atoms 264 Heterogen Atoms 73
Software Software Software Name Purpose PHENIX refinement CrysalisPro data reduction SCALA data scaling PHASER phasing