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KPC-2 CARBAPENEMASE IN COMPLEX WITH THE BORONIC ACID INHIBITOR MB_076
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2OV5
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 100 mM citric acid pH 5.5, 100 mM KSCN, 30 % PEG 6K and 10 mM CdCl2
Crystal Properties Matthews coefficient Solvent content 2.24 45.03
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 51.716 α = 90 b = 66.673 β = 90 c = 73.143 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS EIGER X 9M 2020-12-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS-II BEAMLINE 17-ID-1 0.97933 NSLS-II 17-ID-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.38 28.04 99.6 0.068 0.99 15.5 6.6 52526
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.38 1.42 0.683 0.767 2.2
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 2OV5 1.38 28.04 49772 2688 99.56 0.1489 0.1477 0.1483 0.1703 0.1706 RANDOM 14.161
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.813 r_dihedral_angle_4_deg 13.046 r_dihedral_angle_3_deg 12.84 r_dihedral_angle_1_deg 6.561 r_angle_refined_deg 1.911 r_angle_other_deg 1.621 r_chiral_restr 0.092 r_bond_refined_d 0.013 r_gen_planes_refined 0.011 r_gen_planes_other 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.813 r_dihedral_angle_4_deg 13.046 r_dihedral_angle_3_deg 12.84 r_dihedral_angle_1_deg 6.561 r_angle_refined_deg 1.911 r_angle_other_deg 1.621 r_chiral_restr 0.092 r_bond_refined_d 0.013 r_gen_planes_refined 0.011 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1961 Nucleic Acid Atoms Solvent Atoms 302 Heterogen Atoms 24
Software Software Software Name Purpose XDS data reduction Aimless data scaling REFMAC refinement PDB_EXTRACT data extraction PHASER phasing