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Structure of BlaC from Mycobacterium tuberculosis covalently bound to avibactam.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2GDN
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293.15 0.1 M sodium acetate buffer, pH 5.0
25% w/v PEG1500
Crystal Properties Matthews coefficient Solvent content 2.04 39.84
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 39.52 α = 104.83 b = 41.324 β = 90.03 c = 76.36 γ = 91.18
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 R 4M 2016-11-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID30B 0.9677 ESRF ID30B
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 1.62 73.82 87.3 0.089 0.994 5.8 3.9 51765
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.62 1.65 49.1 0.652 0.578 1.3 3.9
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 2GDN 1.62 73.82 49166 2394 87 0.21066 0.20906 0.2227 0.24393 0.2579 RANDOM 14.727
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] -0.91 -0.02 -0.27 1.18 -0.26 -0.11
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.124 r_dihedral_angle_4_deg 19.228 r_dihedral_angle_3_deg 13.221 r_dihedral_angle_1_deg 6.623 r_long_range_B_refined 3.703 r_long_range_B_other 3.7 r_scangle_other 2.665 r_mcangle_other 2.178 r_mcangle_it 2.177 r_angle_refined_deg 1.858
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.124 r_dihedral_angle_4_deg 19.228 r_dihedral_angle_3_deg 13.221 r_dihedral_angle_1_deg 6.623 r_long_range_B_refined 3.703 r_long_range_B_other 3.7 r_scangle_other 2.665 r_mcangle_other 2.178 r_mcangle_it 2.177 r_angle_refined_deg 1.858 r_scbond_it 1.759 r_scbond_other 1.758 r_mcbond_it 1.426 r_mcbond_other 1.421 r_angle_other_deg 1.087 r_chiral_restr 0.12 r_bond_refined_d 0.018 r_gen_planes_refined 0.009 r_bond_other_d 0.002 r_gen_planes_other 0.002 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4017 Nucleic Acid Atoms Solvent Atoms 138 Heterogen Atoms 55
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling MOLREP phasing