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Crystal Structure of Salmonella FraB Deglycase, Crystal Form 1
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3FKJ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 298 15% v/v 2-propanol, 0.1 M magnesium chloride, 0.1 M MES, pH 6.5
Crystal Properties Matthews coefficient Solvent content 2.34 47.39
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 55.292 α = 90 b = 108.515 β = 90 c = 120.856 γ = 90
Symmetry Space Group P 21 21 21
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 2020-08-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 31-ID 0.97930 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 1.85 80.743 86 0.049 0.021 16.1 6.3 53947
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 1.851 1.975 24.7 1.57 0.648 6.9
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 1.851 80.743 53814 2620 85.724 0.198 0.1955 0.2047 0.2538 0.2634 50.417
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] 0.032 -0.224 0.191
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 16.88 r_dihedral_angle_6_deg 14.412 r_dihedral_angle_2_deg 14.375 r_lrange_it 11.348 r_lrange_other 11.305 r_scangle_it 8.736 r_scangle_other 8.735 r_mcangle_it 7.486 r_mcangle_other 7.485 r_dihedral_angle_1_deg 7.135
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 16.88 r_dihedral_angle_6_deg 14.412 r_dihedral_angle_2_deg 14.375 r_lrange_it 11.348 r_lrange_other 11.305 r_scangle_it 8.736 r_scangle_other 8.735 r_mcangle_it 7.486 r_mcangle_other 7.485 r_dihedral_angle_1_deg 7.135 r_scbond_it 6.163 r_scbond_other 6.161 r_mcbond_it 5.467 r_mcbond_other 5.464 r_angle_refined_deg 1.96 r_angle_other_deg 0.66 r_symmetry_nbd_refined 0.268 r_nbd_other 0.231 r_nbd_refined 0.229 r_xyhbond_nbd_refined 0.2 r_symmetry_nbd_other 0.198 r_nbtor_refined 0.193 r_symmetry_xyhbond_nbd_refined 0.191 r_chiral_restr 0.1 r_symmetry_nbtor_other 0.086 r_symmetry_xyhbond_nbd_other 0.084 r_bond_refined_d 0.009 r_gen_planes_refined 0.009 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4801 Nucleic Acid Atoms Solvent Atoms 273 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling MOLREP phasing