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Crystal structure of AbHpaI-Mg-(4R)-KDGal complex, Class II aldolase, HpaI from Acinetobacter baumannii
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7ET8
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 MICROBATCH 4.6 277 CaCl2, MPD, Na acetate
Crystal Properties Matthews coefficient Solvent content 2.83 56.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 147.565 α = 90 b = 90.353 β = 122.23 c = 86.518 γ = 90
Symmetry Space Group C 1 2 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CMOS BRUKER PHOTON 100 2020-08-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE BRUKER TURBO X-RAY SOURCE 1.54
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 1.8 24.41 99.7 0.121 0.131 0.05 0.995 11 6.7 89082
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 1.8 1.83 97.7 1.033 1.181 0.565 0.562 4.2
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 (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 7ET8 1.9 24.4 71350 3727 99.18 0.1696 0.1681 0.1791 0.1971 0.2057 RANDOM 15.856
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] -0.13 0.17 0.07 -0.08
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.536 r_dihedral_angle_3_deg 13.21 r_dihedral_angle_4_deg 12.999 r_dihedral_angle_1_deg 6.664 r_angle_refined_deg 1.756 r_angle_other_deg 1.494 r_chiral_restr 0.092 r_bond_refined_d 0.012 r_gen_planes_refined 0.01 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.536 r_dihedral_angle_3_deg 13.21 r_dihedral_angle_4_deg 12.999 r_dihedral_angle_1_deg 6.664 r_angle_refined_deg 1.756 r_angle_other_deg 1.494 r_chiral_restr 0.092 r_bond_refined_d 0.012 r_gen_planes_refined 0.01 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5781 Nucleic Acid Atoms Solvent Atoms 652 Heterogen Atoms 40
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PDB_EXTRACT data extraction PROTEUM PLUS data reduction PHASER phasing