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Mandelate oxidase mutant-Y128F with the N5-benzyl-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 3.51 64.94
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 137.843 α = 90 b = 137.843 β = 90 c = 111.84 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 2015-12-05 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 1.65 30 99.3 0.038 0.022 28.41 9.1 63389
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 1.65 1.71 100 0.703 0.303 0.77 1.97 8.8
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 1.65 30 56778 3035 93.33 0.15656 0.15523 0.1688 0.18139 0.1897 RANDOM 19.351
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] -0.18 -0.18 0.35
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.852 r_dihedral_angle_4_deg 14.381 r_dihedral_angle_3_deg 13.385 r_long_range_B_refined 6.625 r_long_range_B_other 6.624 r_dihedral_angle_1_deg 6.344 r_scangle_other 4.74 r_scbond_it 2.996 r_scbond_other 2.995 r_mcangle_other 2.834
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.852 r_dihedral_angle_4_deg 14.381 r_dihedral_angle_3_deg 13.385 r_long_range_B_refined 6.625 r_long_range_B_other 6.624 r_dihedral_angle_1_deg 6.344 r_scangle_other 4.74 r_scbond_it 2.996 r_scbond_other 2.995 r_mcangle_other 2.834 r_mcangle_it 2.831 r_angle_refined_deg 2.535 r_mcbond_it 1.87 r_mcbond_other 1.857 r_angle_other_deg 0.914 r_chiral_restr 0.111 r_bond_refined_d 0.02 r_gen_planes_refined 0.012 r_bond_other_d 0.001 r_gen_planes_other 0.001 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 2485 Nucleic Acid Atoms Solvent Atoms 299 Heterogen Atoms 51
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHENIX phasing