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Crystal Structure of Salmonella FraB Deglycase, E214A Mutant, Crystal Form 5
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 9OTJ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6 298 18% w/v PEG6000, 0.2 M magnesium chloride, 0.1 M MES, pH 6.0
Crystal Properties Matthews coefficient Solvent content 3.77 67.37
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 114.417 α = 90 b = 114.417 β = 90 c = 154.469 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 PIXEL DECTRIS PILATUS3 6M 2022-07-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 31-ID 0.979310 APS 31-ID
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 1.873 99.088 36.7 0.078 0.026 15.8 9.6 35409
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.873 2.152 0.886 0.354 2.2
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1.873 99.088 35409 1718 36.72 0.272 0.2683 0.2734 0.3333 0.3367 40.453
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] -0.022 -0.011 -0.022 0.071
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 18.273 r_dihedral_angle_6_deg 14.564 r_dihedral_angle_1_deg 9.084 r_lrange_it 8.368 r_lrange_other 8.368 r_mcangle_it 5.697 r_mcangle_other 5.696 r_scangle_it 5.525 r_scangle_other 5.525 r_dihedral_angle_2_deg 5.464
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 18.273 r_dihedral_angle_6_deg 14.564 r_dihedral_angle_1_deg 9.084 r_lrange_it 8.368 r_lrange_other 8.368 r_mcangle_it 5.697 r_mcangle_other 5.696 r_scangle_it 5.525 r_scangle_other 5.525 r_dihedral_angle_2_deg 5.464 r_mcbond_it 3.654 r_mcbond_other 3.654 r_scbond_it 3.417 r_scbond_other 3.416 r_angle_refined_deg 1.761 r_angle_other_deg 0.596 r_symmetry_xyhbond_nbd_refined 0.243 r_nbd_refined 0.242 r_symmetry_nbd_other 0.213 r_symmetry_nbd_refined 0.211 r_xyhbond_nbd_refined 0.208 r_nbtor_refined 0.194 r_nbd_other 0.169 r_symmetry_nbtor_other 0.086 r_chiral_restr 0.08 r_symmetry_xyhbond_nbd_other 0.029 r_bond_refined_d 0.006 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4649 Nucleic Acid Atoms Solvent Atoms 60 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling MOLREP phasing