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Crystal structure of cytochrome P450 CYP260A1 (S276I) bound with progesterone
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5LIV
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 293 0.1 M Bis-Tris propane pH 6.5, 19% (w/v) PEG 3350, 0.05 M MgCl2
Crystal Properties Matthews coefficient Solvent content 2.16 43.18
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 100.907 α = 90 b = 64.565 β = 113.07 c = 128.644 γ = 90
Symmetry Space Group C 1 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 2015-11-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID29 0.97625 ESRF ID29
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 1.9 46.42 99.4 0.042 0.048 0.023 0.999 21.7 4.2 59758 26
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 1.9 1.94 99.2 0.421 0.481 0.228 0.86 4.3
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 THROUGHOUT 5liv 1.9 46.418 0.01 59758 5655 99.3 0.1891 0.1871 0.1937 0.229 0.233 32.4238
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 15.368 f_angle_d 1.449 f_chiral_restr 0.076 f_bond_d 0.016 f_plane_restr 0.009
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6138 Nucleic Acid Atoms Solvent Atoms 418 Heterogen Atoms 132
Software Software Software Name Purpose PHENIX refinement EDNA data collection XDS data reduction Aimless data scaling PHASER phasing PDB_EXTRACT data extraction