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Mandelate oxidase mutant-Y128F with the C4a-OH-FMN 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 3.4 63.77
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 138.576 α = 90 b = 138.576 β = 90 c = 107.889 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 2018-07-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSRRC BEAMLINE BL15A1 1.0 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 2.07 30 100 0.05 0.024 30.2 9.3 32246
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 2.07 2.14 99.9 0.52 0.22 0.911 3.3 9.1
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 2.07 30 29522 1561 96.23 0.20681 0.20475 0.2136 0.24618 0.2509 RANDOM 33.796
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] -0.15 -0.15 0.29
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.156 r_dihedral_angle_4_deg 18.522 r_dihedral_angle_3_deg 16.614 r_long_range_B_refined 8.75 r_long_range_B_other 8.748 r_dihedral_angle_1_deg 6.299 r_scangle_other 5.727 r_mcangle_it 4.594 r_mcangle_other 4.593 r_scbond_it 3.706
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.156 r_dihedral_angle_4_deg 18.522 r_dihedral_angle_3_deg 16.614 r_long_range_B_refined 8.75 r_long_range_B_other 8.748 r_dihedral_angle_1_deg 6.299 r_scangle_other 5.727 r_mcangle_it 4.594 r_mcangle_other 4.593 r_scbond_it 3.706 r_scbond_other 3.701 r_mcbond_it 3.189 r_mcbond_other 3.187 r_angle_refined_deg 2.116 r_angle_other_deg 1.146 r_chiral_restr 0.125 r_bond_refined_d 0.021 r_gen_planes_refined 0.012 r_bond_other_d 0.004 r_gen_planes_other 0.003 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2452 Nucleic Acid Atoms Solvent Atoms 74 Heterogen Atoms 32
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing