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Structure of the complex of erythrose-4-phosphate dehydrogenase from Acinetobacter baumannii with nicotinamide adenine dinucleotide at 2.74 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 0.2M AMSO4.6H2O, 0.1M HEPES sodium (pH 7.5)
Crystal Properties Matthews coefficient Solvent content 3.07 59.96
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 147.262 α = 90 b = 167.618 β = 90 c = 151.58 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) 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 2.74 45.96 100 0.42 0.11 0.98 8.3 13.6 49521
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.74 2.83 100 1.98 0.56 0.61 2 13.5
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 2.74 45.96 49489 1536 99.927 0.166 0.1642 0.1701 0.2285 0.2241 40.316
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] 1.591 -1.013 -0.577
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 13.691 r_dihedral_angle_6_deg 13.458 r_lrange_it 8.691 r_dihedral_angle_2_deg 8.683 r_lrange_other 8.678 r_dihedral_angle_1_deg 6.728 r_scangle_it 6.482 r_scangle_other 6.481 r_mcangle_other 4.619 r_mcangle_it 4.617
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 13.691 r_dihedral_angle_6_deg 13.458 r_lrange_it 8.691 r_dihedral_angle_2_deg 8.683 r_lrange_other 8.678 r_dihedral_angle_1_deg 6.728 r_scangle_it 6.482 r_scangle_other 6.481 r_mcangle_other 4.619 r_mcangle_it 4.617 r_scbond_it 3.96 r_scbond_other 3.959 r_mcbond_it 2.873 r_mcbond_other 2.865 r_angle_refined_deg 1.384 r_angle_other_deg 0.487 r_nbd_other 0.302 r_symmetry_nbd_refined 0.217 r_symmetry_nbd_other 0.215 r_dihedral_angle_other_2_deg 0.213 r_nbd_refined 0.196 r_nbtor_refined 0.175 r_xyhbond_nbd_refined 0.155 r_symmetry_xyhbond_nbd_other 0.093 r_symmetry_nbtor_other 0.082 r_symmetry_xyhbond_nbd_refined 0.071 r_chiral_restr 0.065 r_bond_refined_d 0.005 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 10716 Nucleic Acid Atoms Solvent Atoms 445 Heterogen Atoms 196
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling MOLREP phasing Coot model building