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Crystal structure of the complex of glyceraldehyde-3-phosphate dehydrogenase of type B from Acinetobacter baumannii with Adenosine monophosphate at 3.20 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 0.2M MgSo4. 6H2O, 0.1M HEPES sodium (pH 7.5)
Crystal Properties Matthews coefficient Solvent content 3.06 59.83
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 147.509 α = 90 b = 167.732 β = 90 c = 150.726 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 3.2 89.26 97.2 0.23 0.24 0.069 0.998 7.9 12.8 30330
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 3.2 3.37 99.7 2.39 2.51 0.757 0.86 1.1 10.9
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 3.2 84.007 30303 1202 97.181 0.204 0.2012 0.2115 0.2793 0.2768 129.269
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] 12.992 -18.822 5.831
RMS Deviations Key Refinement Restraint Deviation r_lrange_it 15.651 r_lrange_other 15.651 r_dihedral_angle_3_deg 14.152 r_dihedral_angle_6_deg 12.489 r_scangle_it 11.558 r_scangle_other 11.557 r_mcangle_it 11.256 r_mcangle_other 11.256 r_dihedral_angle_1_deg 7.284 r_mcbond_it 7.172
RMS Deviations Key Refinement Restraint Deviation r_lrange_it 15.651 r_lrange_other 15.651 r_dihedral_angle_3_deg 14.152 r_dihedral_angle_6_deg 12.489 r_scangle_it 11.558 r_scangle_other 11.557 r_mcangle_it 11.256 r_mcangle_other 11.256 r_dihedral_angle_1_deg 7.284 r_mcbond_it 7.172 r_mcbond_other 7.172 r_scbond_it 7.01 r_scbond_other 7.007 r_dihedral_angle_2_deg 5.483 r_angle_refined_deg 1.112 r_dihedral_angle_other_2_deg 0.853 r_angle_other_deg 0.402 r_nbd_other 0.224 r_nbd_refined 0.212 r_symmetry_nbd_other 0.212 r_symmetry_xyhbond_nbd_refined 0.188 r_nbtor_refined 0.175 r_xyhbond_nbd_refined 0.161 r_symmetry_nbd_refined 0.148 r_symmetry_nbtor_other 0.079 r_chiral_restr 0.05 r_symmetry_xyhbond_nbd_other 0.027 r_bond_refined_d 0.003 r_gen_planes_refined 0.003 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 89 Heterogen Atoms 122
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling MOLREP phasing Coot model building