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The 2.2 A crystal structure of CYP109E1 from Bacillus megaterium bound with four corticosterone molecules
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, HANGING DROP 293 20% PEG 3350, 0.1 M Bis-Tris, pH 6.5 and 4% tacsimate reagent (pH 6.0)
Crystal Properties Matthews coefficient Solvent content 3.08 60.08
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 120.418 α = 90 b = 120.418 β = 90 c = 140.803 γ = 120
Symmetry Space Group P 32 2 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 DECTRIS PILATUS 6M-F 2014-04-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-2 0.87261 ESRF ID23-2
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 2.2 48.9 99.7 0.087 0.998 15.9 5.9 60153 32.87
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.2 2.26 100 0.669 5.9
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 2.2 46.934 0.18 60153 5833 99.72 0.1872 0.1848 0.194 0.2321 0.2356 42.3849
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 12.823 f_angle_d 1.322 f_chiral_restr 0.063 f_bond_d 0.014 f_plane_restr 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6389 Nucleic Acid Atoms Solvent Atoms 197 Heterogen Atoms 286
Software Software Software Name Purpose EDNA data collection XDS data reduction Aimless data scaling PHENIX refinement PDB_EXTRACT data extraction PHASER phasing