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Cryo structure of Mycobacterium tuberculosis beta lactamase microcrystals mixed with sulbactam for 3 hours
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6B5X
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.1 300 2.1 M Ammonium Phosphate
Crystal Properties Matthews coefficient Solvent content 3.57 65.52
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 79.442 α = 90 b = 96.666 β = 108.082 c = 111.028 γ = 90
Symmetry Space Group P 1 21 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 PIXEL DECTRIS PILATUS 6M 2021-04-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID 1.26 APS 19-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 2.6 48.33 100 0.18 0.372 2.7 25400
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.6 2.64 0.18
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 6b5x 2.736 48.33 25399 1322 60.032 0.214 0.2111 0.2111 0.2682 0.2684 57.967
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] -1.683 -0.896 2.15 0.098
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 16.443 r_dihedral_angle_6_deg 15.141 r_dihedral_angle_2_deg 13.509 r_lrange_it 11.725 r_lrange_other 11.718 r_dihedral_angle_1_deg 9.369 r_scangle_it 5.646 r_scangle_other 5.646 r_mcangle_it 4.92 r_mcangle_other 4.919
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 16.443 r_dihedral_angle_6_deg 15.141 r_dihedral_angle_2_deg 13.509 r_lrange_it 11.725 r_lrange_other 11.718 r_dihedral_angle_1_deg 9.369 r_scangle_it 5.646 r_scangle_other 5.646 r_mcangle_it 4.92 r_mcangle_other 4.919 r_scbond_it 3.331 r_scbond_other 3.331 r_mcbond_it 3.008 r_mcbond_other 3.006 r_angle_refined_deg 1.191 r_angle_other_deg 0.417 r_nbd_other 0.252 r_symmetry_nbd_refined 0.245 r_xyhbond_nbd_refined 0.236 r_nbd_refined 0.216 r_symmetry_xyhbond_nbd_refined 0.216 r_symmetry_nbd_other 0.198 r_nbtor_refined 0.172 r_ncsr_local_group_4 0.112 r_ncsr_local_group_1 0.11 r_ncsr_local_group_6 0.107 r_ncsr_local_group_3 0.106 r_ncsr_local_group_2 0.101 r_ncsr_local_group_5 0.099 r_symmetry_nbtor_other 0.081 r_symmetry_xyhbond_nbd_other 0.068 r_chiral_restr 0.052 r_bond_refined_d 0.005 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7952 Nucleic Acid Atoms Solvent Atoms 156 Heterogen Atoms 80
Software Software Software Name Purpose REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling PHASER phasing