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Mandelate oxidase with the enoyl FMN epoxide adduct
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3SGZ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 293 35% Tascimate, 0.1M Bis-Tris propane pH 7.0
Crystal Properties Matthews coefficient Solvent content 3.5 64.88
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 137.541 α = 90 b = 137.541 β = 90 c = 112.18 γ = 90
Symmetry Space Group I 4 2 2
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 RAYONIX MX300HE 2017-08-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSRRC BEAMLINE BL15A1 1 NSRRC BL15A1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) 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 1.7 30 99 0.037 0.018 34.4 9.8 58282
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.7 1.76 99.9 0.65 0.25 0.803 2.4 9.7
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) 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 THROUGHOUT 3SGZ 1.7 26.99 53954 2913 96.52 0.1659 0.1647 0.1763 0.1873 0.196 RANDOM 20.096
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] -0.09 -0.09 0.17
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 26.852 r_dihedral_angle_4_deg 16.981 r_dihedral_angle_3_deg 14.846 r_dihedral_angle_1_deg 6.141 r_angle_refined_deg 2.11 r_angle_other_deg 1.159 r_chiral_restr 0.109 r_bond_refined_d 0.018 r_gen_planes_refined 0.011 r_gen_planes_other 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 26.852 r_dihedral_angle_4_deg 16.981 r_dihedral_angle_3_deg 14.846 r_dihedral_angle_1_deg 6.141 r_angle_refined_deg 2.11 r_angle_other_deg 1.159 r_chiral_restr 0.109 r_bond_refined_d 0.018 r_gen_planes_refined 0.011 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2490 Nucleic Acid Atoms Solvent Atoms 346 Heterogen Atoms 36
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHENIX phasing