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Structure of the complex of erythrose-4-phosphate dehydrogenase from Acinetobacter baumannii with nicotinamide adenine dinucleotide in the presence of poly(ethylene glycol) at 2.20 A 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 EVAPORATION 7.5 298 0.2 M MgCl2.6H2O, 0.1M HEPES sodium (pH 7.5), 30% v/v PEG 400
Crystal Properties Matthews coefficient Solvent content 2.98 58.78
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 145.365 α = 90 b = 167.131 β = 90 c = 149.592 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 298 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 0.87313 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 2.2 88.454 98.9 0.23 0.23 0.064 0.997 9.3 13.9 91060
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 2.2 2.24 98.1 2.38 2.46 0.64 0.725 1.8 14.4
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 2.2 88.454 91025 1335 98.692 0.169 0.1683 0.1746 0.2167 0.2197 45.029
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] -0.197 0.111 0.085
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 14.178 r_dihedral_angle_3_deg 13.59 r_lrange_other 9.381 r_lrange_it 9.377 r_dihedral_angle_2_deg 9.111 r_scangle_it 7.336 r_scangle_other 7.335 r_dihedral_angle_1_deg 7.108 r_mcangle_it 5.087 r_mcangle_other 5.086
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 14.178 r_dihedral_angle_3_deg 13.59 r_lrange_other 9.381 r_lrange_it 9.377 r_dihedral_angle_2_deg 9.111 r_scangle_it 7.336 r_scangle_other 7.335 r_dihedral_angle_1_deg 7.108 r_mcangle_it 5.087 r_mcangle_other 5.086 r_scbond_it 4.775 r_scbond_other 4.775 r_mcbond_it 3.525 r_mcbond_other 3.524 r_angle_refined_deg 1.527 r_angle_other_deg 0.514 r_dihedral_angle_other_2_deg 0.279 r_nbd_other 0.229 r_symmetry_nbd_other 0.216 r_symmetry_nbd_refined 0.207 r_nbd_refined 0.204 r_nbtor_refined 0.178 r_xyhbond_nbd_refined 0.167 r_symmetry_xyhbond_nbd_refined 0.11 r_symmetry_nbtor_other 0.085 r_chiral_restr 0.069 r_bond_refined_d 0.007 r_gen_planes_refined 0.006 r_symmetry_xyhbond_nbd_other 0.004 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 10716 Nucleic Acid Atoms Solvent Atoms 623 Heterogen Atoms 443
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling MOLREP phasing Coot model building