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Crystal structure of Adenosine triphosphate phosphoribosyltransferase (HisG) from Acinetobacter baumannii at 2.975 A resolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7WGM
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.6 298 0.1M Sodium acetate trihydrate (pH 4.6), 2M Sodium formate
Crystal Properties Matthews coefficient Solvent content 2.63 53.24
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 69.698 α = 90 b = 77.833 β = 90 c = 97.239 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 EIGER X 4M 2022-01-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE MASSIF-3 0.968 ESRF MASSIF-3
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) CC (Half) 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 2.975 60.765 90.5 0.052 0.998 8.6 4.2 6663 100.6
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.975 3.26 73.2 0.756 1.6 3
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 7WGM 2.975 60.765 6662 304 58.706 0.224 0.2205 0.2222 0.2966 0.2949 102.361
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] 0.72 0.174 -0.895
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.532 r_lrange_it 16.653 r_lrange_other 16.653 r_dihedral_angle_3_deg 14.798 r_dihedral_angle_4_deg 13.335 r_mcangle_it 8.738 r_mcangle_other 8.738 r_scangle_it 8.723 r_scangle_other 8.722 r_dihedral_angle_1_deg 8.167
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.532 r_lrange_it 16.653 r_lrange_other 16.653 r_dihedral_angle_3_deg 14.798 r_dihedral_angle_4_deg 13.335 r_mcangle_it 8.738 r_mcangle_other 8.738 r_scangle_it 8.723 r_scangle_other 8.722 r_dihedral_angle_1_deg 8.167 r_mcbond_it 5.354 r_mcbond_other 5.352 r_scbond_it 5.163 r_scbond_other 5.162 r_angle_other_deg 2.233 r_angle_refined_deg 1.293 r_symmetry_nbd_refined 0.273 r_symmetry_xyhbond_nbd_refined 0.27 r_nbd_other 0.266 r_symmetry_nbd_other 0.217 r_nbd_refined 0.21 r_ncsr_local_group_1 0.154 r_nbtor_refined 0.15 r_xyhbond_nbd_refined 0.127 r_symmetry_xyhbond_nbd_other 0.07 r_symmetry_nbtor_other 0.064 r_chiral_restr 0.048 r_bond_other_d 0.034 r_gen_planes_refined 0.005 r_bond_refined_d 0.004 r_gen_planes_other 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3518 Nucleic Acid Atoms Solvent Atoms 24 Heterogen Atoms 9
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling MOLREP phasing