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Structure of erythrose-4-phosphate dehydrogenase from Acinetobacter baumannii at 3.00 A resolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3CMC
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 EVAPORATION 7.5 298 A reservoir solution containing 0.2 M MgCl2.6H2O, 0.1 M HEPES sodium (pH 7.5), and 30% v/v PEG 400 was prepared.
Crystal Properties Matthews coefficient Solvent content 3.1 60.31
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 147.646 α = 90 b = 167.88 β = 90 c = 152.269 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 3 49.536 100 0.73 0.79 0.21 0.971 7.3 13.5 38162
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 3 3.13 100 2.86 2.98 0.78 0.69 1.9 14.4
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 3CMC 3 49.536 38116 754 99.893 0.167 0.1658 0.1736 0.2419 0.2417 48.146
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] -0.227 -3.798 4.025
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 14.348 r_dihedral_angle_6_deg 13.206 r_lrange_it 9.201 r_lrange_other 9.2 r_dihedral_angle_2_deg 8.761 r_dihedral_angle_1_deg 6.871 r_scangle_it 6.858 r_scangle_other 6.845 r_mcangle_it 5.405 r_mcangle_other 5.405
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 14.348 r_dihedral_angle_6_deg 13.206 r_lrange_it 9.201 r_lrange_other 9.2 r_dihedral_angle_2_deg 8.761 r_dihedral_angle_1_deg 6.871 r_scangle_it 6.858 r_scangle_other 6.845 r_mcangle_it 5.405 r_mcangle_other 5.405 r_scbond_it 4.209 r_scbond_other 4.2 r_mcbond_it 3.379 r_mcbond_other 3.377 r_angle_refined_deg 1.499 r_angle_other_deg 0.506 r_dihedral_angle_other_2_deg 0.435 r_nbd_other 0.349 r_symmetry_nbd_other 0.212 r_nbd_refined 0.209 r_nbtor_refined 0.18 r_symmetry_nbd_refined 0.169 r_xyhbond_nbd_refined 0.167 r_symmetry_nbtor_other 0.083 r_chiral_restr 0.065 r_symmetry_xyhbond_nbd_other 0.031 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 10716 Nucleic Acid Atoms Solvent Atoms 265 Heterogen Atoms 216
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling MOLREP phasing Coot model building