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Crystal structure of Poly(ethylene glycol) stabilized erythrose-4-phosphate dehydrogenase from Acinetobacter baumannii at 2.30 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 59.04
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 145.775 α = 90 b = 167.135 β = 90 c = 150.103 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 2.3 46.703 100 0.2 0.02 0.06 0.998 11.2 13.2 81357
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 2.3 2.34 100 1.58 1.69 0.47 0.82 2.2 12.6
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-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 3CMC 2.3 46.703 81321 2400 99.963 0.153 0.1517 0.201 0.1883 44.028
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] 1.561 -3.614 2.053
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 14.571 r_dihedral_angle_3_deg 13.205 r_lrange_it 9.593 r_lrange_other 9.584 r_dihedral_angle_2_deg 8.827 r_scangle_it 7.528 r_scangle_other 7.528 r_dihedral_angle_1_deg 7.008 r_mcangle_it 5.144 r_mcangle_other 5.143
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 14.571 r_dihedral_angle_3_deg 13.205 r_lrange_it 9.593 r_lrange_other 9.584 r_dihedral_angle_2_deg 8.827 r_scangle_it 7.528 r_scangle_other 7.528 r_dihedral_angle_1_deg 7.008 r_mcangle_it 5.144 r_mcangle_other 5.143 r_scbond_it 4.988 r_scbond_other 4.988 r_mcbond_it 3.591 r_mcbond_other 3.59 r_angle_refined_deg 1.547 r_angle_other_deg 0.52 r_metal_ion_refined 0.259 r_dihedral_angle_other_2_deg 0.241 r_symmetry_nbd_other 0.214 r_nbd_other 0.203 r_nbd_refined 0.201 r_symmetry_nbd_refined 0.184 r_nbtor_refined 0.176 r_symmetry_xyhbond_nbd_refined 0.171 r_xyhbond_nbd_refined 0.162 r_symmetry_nbtor_other 0.085 r_chiral_restr 0.071 r_symmetry_xyhbond_nbd_other 0.023 r_bond_refined_d 0.007 r_gen_planes_refined 0.007 r_bond_other_d 0.005 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 10716 Nucleic Acid Atoms Solvent Atoms 641 Heterogen Atoms 488
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling MOLREP phasing Coot model building