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P450 (OxyA) from kistamicin biosynthesis, Y99F mutant
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model PHYRE PHYRE Model
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 298.15 0.1 M MMT, pH 6.0, 25% PEG1500
Crystal Properties Matthews coefficient Solvent content 2.37 43.49
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 69.801 α = 90 b = 69.801 β = 90 c = 132.356 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 CCD ADSC QUANTUM 210r 2018-07-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON AUSTRALIAN SYNCHROTRON BEAMLINE MX1 0.953700 Australian Synchrotron MX1
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 1.8 44.63 99.9 0.057 0.063 0.027 0.999 15.4 5.4 35272 26.0371633274
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 1.8 1.84 0.897 0.995 0.422 0.657 1.5
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 PHYRE Model 1.80159202452 35.6367186788 1.34350040492 35221 1679 99.8922260983 0.185905701289 0.184039624568 0.1869 0.223911407816 0.2245 32.9332473469
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 18.6427307161 f_angle_d 0.779019883 f_chiral_restr 0.0417846482138 f_bond_d 0.0047199580901 f_plane_restr 0.00428236133013
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2732 Nucleic Acid Atoms Solvent Atoms 168 Heterogen Atoms 49
Software Software Software Name Purpose PHENIX refinement PHENIX refinement XDS data reduction Aimless data scaling PHENIX phasing