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Crystal structure of P450BytO from Planomonospora sp.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5GNL
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 293 0.2 M Ammonium formate, 20% PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.32 42.26
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 44.186 α = 90 b = 96.586 β = 105.767 c = 45.148 γ = 90
Symmetry Space Group P 1 21 1
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-6000HE 2024-03-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU 1.542
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 1.9 20.67 99.03 0.998 28.32 3.6 28465 11.53
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 1.9 1.968 0.976
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 3A4G 1.9 20.67 1.45 28463 1352 99.12 0.1643 0.1626 0.1627 0.1984 0.1984 RANDOM 14.43
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 8.2927 f_angle_d 0.9748 f_chiral_restr 0.0544 f_plane_restr 0.0086 f_bond_d 0.0068
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2837 Nucleic Acid Atoms Solvent Atoms 489 Heterogen Atoms 43
Software Software Software Name Purpose PHENIX refinement XDS data reduction Aimless data scaling PHASER phasing