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Structure of G132S BlaC from Mycobacterium tuberculosis bound to the trans-enamine adduct of sulbactam
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6H2K
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.3 293 0.1 M Sodium Cacodylate, 15% PEG-SB, 10% Ethylene Glycol, 5% TMate
Crystal Properties Matthews coefficient Solvent content 2.02 38.97
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 53.488 α = 90 b = 54.658 β = 90 c = 78.202 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 2020-02-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 0.912 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 1.3 78.2 98.2 0.038 0.999 11.1 5.7 56098
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 1.3 1.32 0.582 0.655 1.3 5.6
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 6H2K 1.3 44.84 53380 2648 98.08 0.154 0.15221 0.1581 0.18938 0.1643 RANDOM 14.333
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] 1.33 1.08 -2.42
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.665 r_dihedral_angle_4_deg 18.593 r_dihedral_angle_3_deg 10.994 r_dihedral_angle_1_deg 6.586 r_rigid_bond_restr 3.921 r_long_range_B_refined 2.285 r_long_range_B_other 2.15 r_scangle_other 2.063 r_angle_refined_deg 1.94 r_scbond_it 1.719
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.665 r_dihedral_angle_4_deg 18.593 r_dihedral_angle_3_deg 10.994 r_dihedral_angle_1_deg 6.586 r_rigid_bond_restr 3.921 r_long_range_B_refined 2.285 r_long_range_B_other 2.15 r_scangle_other 2.063 r_angle_refined_deg 1.94 r_scbond_it 1.719 r_scbond_other 1.719 r_angle_other_deg 1.686 r_mcangle_it 1.489 r_mcangle_other 1.489 r_mcbond_it 1.168 r_mcbond_other 1.168 r_chiral_restr 0.113 r_bond_refined_d 0.016 r_gen_planes_refined 0.012 r_bond_other_d 0.001 r_gen_planes_other 0.001 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_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1994 Nucleic Acid Atoms Solvent Atoms 221 Heterogen Atoms 37
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling MOLREP phasing