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Crystal structure of the complex of erythrose-4-phosphate dehydrogenase from Acinetobacter baumannii with Adenosine monophosphate at 2.40 Angstrom resolution.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8ZN4
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 298 0.2 M MgSO4.6H2O, 0.1 M HEPES sodium (pH 7.5)
Crystal Properties Matthews coefficient Solvent content 3.15 61.02
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 147.578 α = 90 b = 167.012 β = 90 c = 155.058 γ = 90
Symmetry Space Group C 2 2 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 EIGER2 X 9M 2023-07-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID30B 0.8731 ESRF ID30B
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 2.4 83.51 100 0.214 0.228 0.074 0.996 7.6 9.1 74905
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.4 2.45 100 2.055 2.175 0.705 0.602 1 9.2
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 2.4 83.51 74868 1111 99.944 0.172 0.1716 0.1794 0.221 0.2271 49.866
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] 0.108 -0.058 -0.05
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 14.872 r_dihedral_angle_6_deg 14.592 r_lrange_it 10.008 r_lrange_other 10.001 r_scangle_other 8.084 r_scangle_it 8.082 r_dihedral_angle_2_deg 7.986 r_dihedral_angle_1_deg 7.239 r_mcangle_it 5.8 r_mcangle_other 5.799
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 14.872 r_dihedral_angle_6_deg 14.592 r_lrange_it 10.008 r_lrange_other 10.001 r_scangle_other 8.084 r_scangle_it 8.082 r_dihedral_angle_2_deg 7.986 r_dihedral_angle_1_deg 7.239 r_mcangle_it 5.8 r_mcangle_other 5.799 r_scbond_it 5.08 r_scbond_other 5.08 r_mcbond_it 3.903 r_mcbond_other 3.902 r_angle_refined_deg 1.52 r_angle_other_deg 0.508 r_nbd_other 0.215 r_symmetry_nbd_other 0.21 r_nbd_refined 0.205 r_symmetry_nbd_refined 0.188 r_dihedral_angle_other_2_deg 0.18 r_nbtor_refined 0.177 r_symmetry_xyhbond_nbd_refined 0.16 r_xyhbond_nbd_refined 0.154 r_symmetry_nbtor_other 0.083 r_chiral_restr 0.066 r_symmetry_xyhbond_nbd_other 0.045 r_bond_refined_d 0.006 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 10692 Nucleic Acid Atoms Solvent Atoms 707 Heterogen Atoms 124
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling MOLREP phasing Coot model building