☰ Navigation Tabs
Structure of BlaC from Mycobacterium tuberculosis in complex with vaborbactam
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 8.5 293 0.1M MES/Imidazole buffer pH 8.5, 30% w/v EDO-P8K, 0.09M NPS (sodium nitrate, disodium hydrogen phosphate, ammonium sulfate)
Crystal Properties Matthews coefficient Solvent content 2.01 38.66
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 53.49 α = 90 b = 54.656 β = 90 c = 78.109 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 PILATUS 6M-F 2020-12-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 0.9795 Diamond I04-1
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 1.95 44.82 99.9 0.124 0.985 6.5 1.9 17259
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 1.95 2 0.566 0.703 1.3
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 1.95 44.82 16408 847 99.93 0.19027 0.18822 0.2 0.22972 0.2317 RANDOM 28.154
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] -3.05 -3 6.06
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 12.496 r_dihedral_angle_2_deg 6.901 r_dihedral_angle_1_deg 6.878 r_long_range_B_refined 6.615 r_long_range_B_other 6.316 r_scangle_other 3.858 r_mcangle_it 3.035 r_mcangle_other 3.034 r_scbond_it 3.011 r_scbond_other 2.689
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 12.496 r_dihedral_angle_2_deg 6.901 r_dihedral_angle_1_deg 6.878 r_long_range_B_refined 6.615 r_long_range_B_other 6.316 r_scangle_other 3.858 r_mcangle_it 3.035 r_mcangle_other 3.034 r_scbond_it 3.011 r_scbond_other 2.689 r_mcbond_it 2.168 r_mcbond_other 2.161 r_angle_refined_deg 1.523 r_angle_other_deg 0.495 r_chiral_restr 0.066 r_bond_refined_d 0.008 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_dihedral_angle_4_deg 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 1988 Nucleic Acid Atoms Solvent Atoms 140 Heterogen Atoms 80
Software Software Software Name Purpose REFMAC refinement DIALS data reduction Aimless data scaling MOLREP phasing