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Crystal Structure of Salmonella FraB Deglycase, Crystal Form 3
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, 0.1 M MES, pH 6.0-6.5
Crystal Properties Matthews coefficient Solvent content 2.41 49.03
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 58.574 α = 90 b = 110.614 β = 90 c = 115.53 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 2021-03-24 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 1.669 79.9 76.4 0.076 0.022 16.7 12.9 67143
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 1.67 1.828 1.419 0.442 1.6
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 1.669 79.897 67143 3329 76.39 0.172 0.1708 0.1811 0.2021 0.2119 31.89
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] 0.126 -0.099 -0.027
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 14.508 r_dihedral_angle_3_deg 13.821 r_dihedral_angle_2_deg 8.232 r_lrange_it 7.827 r_lrange_other 7.744 r_dihedral_angle_1_deg 6.527 r_scangle_it 6.448 r_scangle_other 6.447 r_scbond_it 4.256 r_scbond_other 4.252
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 14.508 r_dihedral_angle_3_deg 13.821 r_dihedral_angle_2_deg 8.232 r_lrange_it 7.827 r_lrange_other 7.744 r_dihedral_angle_1_deg 6.527 r_scangle_it 6.448 r_scangle_other 6.447 r_scbond_it 4.256 r_scbond_other 4.252 r_mcangle_it 3.885 r_mcangle_other 3.884 r_mcbond_it 2.947 r_mcbond_other 2.945 r_angle_refined_deg 1.712 r_angle_other_deg 0.6 r_nbd_refined 0.22 r_symmetry_nbd_other 0.189 r_nbtor_refined 0.186 r_xyhbond_nbd_refined 0.169 r_nbd_other 0.156 r_symmetry_xyhbond_nbd_refined 0.143 r_symmetry_xyhbond_nbd_other 0.128 r_symmetry_nbd_refined 0.1 r_chiral_restr 0.095 r_symmetry_nbtor_other 0.079 r_bond_refined_d 0.008 r_gen_planes_refined 0.008 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4831 Nucleic Acid Atoms Solvent Atoms 414 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling MOLREP phasing