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Crystal structure of substrate-free CYP109A2 from Bacillus megaterium
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5L90
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 293 1.9M ammonium sulfate, 0.1M HEPES pH 7.5, 2% (v/v) PEG400
Crystal Properties Matthews coefficient Solvent content 2.52 51.26
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 77.125 α = 90 b = 155.534 β = 90 c = 158.151 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 DECTRIS PILATUS 6M 2014-04-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-2 0.873 ESRF ID23-2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 2.7 52.03 97.3 0.112 0.124 0.05 0.996 12.4 5.6 51368 48.76
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.7 2.78 98.5 1.025 1.126 0.458 0.523 5.7
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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 5l90 2.7 49.927 1.1 51368 5009 97.29 0.2264 0.2238 0.2328 0.2751 0.2797 45.9872
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 15.943 f_angle_d 1.418 f_chiral_restr 0.07 f_bond_d 0.018 f_plane_restr 0.01
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 12444 Nucleic Acid Atoms Solvent Atoms 15 Heterogen Atoms 267
Software Software Software Name Purpose EDNA data collection XDS data reduction Aimless data scaling PHASER phasing PHENIX refinement PDB_EXTRACT data extraction