☰ Navigation Tabs
Crystal Structure of Salmonella FraB Deglycase, Crystal Form 1
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 298 10-14% v/v PEG300, 0.1bM MES, pH 6.0-6.5
Crystal Properties Matthews coefficient Solvent content 2.33 47.24
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 57.708 α = 90 b = 109.334 β = 90 c = 114.53 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 2023-04-06 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 1.483 79.084 77.3 0.068 0.029 11.2 6.7 93089
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 1.483 1.601 0.816 0.368
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 1.483 79.084 93089 4610 77.255 0.17 0.1686 0.1684 0.2014 0.2014 21.571
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] -0.021 -0.025 0.046
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.367 r_dihedral_angle_3_deg 12.905 r_dihedral_angle_2_deg 7.464 r_lrange_it 7.236 r_lrange_other 7.155 r_dihedral_angle_1_deg 6.305 r_scangle_it 5.811 r_scangle_other 5.811 r_scbond_it 3.778 r_scbond_other 3.778
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.367 r_dihedral_angle_3_deg 12.905 r_dihedral_angle_2_deg 7.464 r_lrange_it 7.236 r_lrange_other 7.155 r_dihedral_angle_1_deg 6.305 r_scangle_it 5.811 r_scangle_other 5.811 r_scbond_it 3.778 r_scbond_other 3.778 r_mcangle_it 3.264 r_mcangle_other 3.264 r_mcbond_it 2.276 r_mcbond_other 2.276 r_angle_refined_deg 1.82 r_angle_other_deg 0.605 r_symmetry_xyhbond_nbd_other 0.265 r_nbd_refined 0.23 r_symmetry_nbd_refined 0.22 r_symmetry_nbd_other 0.19 r_nbtor_refined 0.188 r_xyhbond_nbd_refined 0.171 r_nbd_other 0.154 r_symmetry_xyhbond_nbd_refined 0.116 r_chiral_restr 0.092 r_symmetry_nbtor_other 0.079 r_gen_planes_refined 0.01 r_bond_refined_d 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 4818 Nucleic Acid Atoms Solvent Atoms 476 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling MOLREP phasing