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Crystal structure of AbHpaI-Mn-pyruvate-succinic semialdehyde 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 4.6 288 CaCl2, MPD, Na acetate
Crystal Properties Matthews coefficient Solvent content 2.76 55.44
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 147.255 α = 90 b = 89.285 β = 122.74 c = 86.135 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 2017-05-18 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 1.98 20.66 94.7 0.068 0.072 0.024 0.998 18.9 7.7 61472
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 1.98 2.04 68.8 0.209 0.26 0.152 0.966 2.4
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 (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 2 20.65 53916 5641 93.95 0.1906 0.1869 0.1982 0.2259 0.2351 RANDOM 14.893
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] -0.17 0.2 -0.07 -0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.871 r_dihedral_angle_3_deg 13.533 r_dihedral_angle_4_deg 12.176 r_dihedral_angle_1_deg 6.64 r_angle_refined_deg 1.568 r_angle_other_deg 1.431 r_chiral_restr 0.085 r_bond_refined_d 0.011 r_gen_planes_refined 0.008 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.871 r_dihedral_angle_3_deg 13.533 r_dihedral_angle_4_deg 12.176 r_dihedral_angle_1_deg 6.64 r_angle_refined_deg 1.568 r_angle_other_deg 1.431 r_chiral_restr 0.085 r_bond_refined_d 0.011 r_gen_planes_refined 0.008 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 385 Heterogen Atoms 43
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PDB_EXTRACT data extraction PROTEUM PLUS data reduction PHASER phasing