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The crystal structure of Mandelate oxidase mutant Y128F with b-Phenyllactate
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 3.49 64.75
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 138.259 α = 90 b = 138.259 β = 90 c = 111.385 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 Bruker DIP-6040 2016-04-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL44XU 1 SPring-8 BL44XU
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 1.8 30 99.9 0.048 0.023 34.5 11.1 49996
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 1.8 1.86 100 0.8 0.32 0.852 2.7 10.7
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 1.8 30 46666 2511 98.2 0.16007 0.1589 0.1718 0.18187 0.1893 RANDOM 25.616
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] -0.04 -0.04 0.07
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.791 r_dihedral_angle_3_deg 13.812 r_dihedral_angle_4_deg 12.459 r_long_range_B_refined 7.922 r_long_range_B_other 7.921 r_scangle_other 6.42 r_dihedral_angle_1_deg 6.419 r_scbond_it 4.209 r_scbond_other 4.208 r_mcangle_it 3.697
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.791 r_dihedral_angle_3_deg 13.812 r_dihedral_angle_4_deg 12.459 r_long_range_B_refined 7.922 r_long_range_B_other 7.921 r_scangle_other 6.42 r_dihedral_angle_1_deg 6.419 r_scbond_it 4.209 r_scbond_other 4.208 r_mcangle_it 3.697 r_mcangle_other 3.686 r_mcbond_it 2.613 r_mcbond_other 2.612 r_angle_refined_deg 2.044 r_angle_other_deg 0.941 r_chiral_restr 0.128 r_bond_refined_d 0.021 r_gen_planes_refined 0.01 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 2470 Nucleic Acid Atoms Solvent Atoms 288 Heterogen Atoms 55
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHENIX phasing