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X-ray structure of cytochrome P450 OleT from Lacicoccus alkaliphilus in complex with icosanoic acid
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4L54
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293.15 Enzyme 10 mg/mL and icosanoic acid 1 mM
in 0.1 M NaCl, 0.1 M HEPES pH7.5 and 3.5 M Sodium formate
Crystal Properties Matthews coefficient Solvent content 3.87 68.2
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 82.799 α = 90 b = 188.859 β = 90 c = 198.313 γ = 90
Symmetry Space Group I 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 DECTRIS EIGER X 16M 2021-06-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL44XU 0.90000 SPring-8 BL44XU
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 2.44 50 99 0.076 0.998 13.51 3.5 58908 24.44
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.44 2.59 97.9 0.783 0.791 1.62 6.89
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 2.44 42.63 1.27 57875 5578 98.97 0.1844 0.182 0.1821 0.2296 0.2294
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 12.9521 f_angle_d 1.0169 f_chiral_restr 0.0539 f_plane_restr 0.0089 f_bond_d 0.0086
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6906 Nucleic Acid Atoms Solvent Atoms 557 Heterogen Atoms 166
Software Software Software Name Purpose PHENIX refinement XDS data reduction XSCALE data scaling PHASER phasing