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Structure of P167S BlaC from Mycobacterium tuberculosis at pH 6.3
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 6.3 293 0.1 M Na Cacod 6.3 pH (Buffer)
1.02 M Na3 Cit (Precipitant)
Crystal Properties Matthews coefficient Solvent content 2.02 38.98
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 40.627 α = 88.19 b = 53.693 β = 69.58 c = 56.273 γ = 87.73
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 EIGER2 XE 16M 2021-09-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.9795 Diamond I04
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.8 53.64 96 0.999 14 2 39659
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.8 1.84 94.9 0.864
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 1.8 38.09 38298 1349 95.98 0.16032 0.15918 0.1718 0.18724 0.1902 RANDOM 21.383
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] 1.96 0.37 -0.09 -1.21 -0.01 -0.61
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 13.099 r_dihedral_angle_2_deg 8.332 r_dihedral_angle_1_deg 6.899 r_long_range_B_refined 5.921 r_long_range_B_other 5.867 r_scangle_other 4.195 r_mcangle_it 3.108 r_mcangle_other 3.108 r_scbond_it 2.815 r_scbond_other 2.815
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 13.099 r_dihedral_angle_2_deg 8.332 r_dihedral_angle_1_deg 6.899 r_long_range_B_refined 5.921 r_long_range_B_other 5.867 r_scangle_other 4.195 r_mcangle_it 3.108 r_mcangle_other 3.108 r_scbond_it 2.815 r_scbond_other 2.815 r_mcbond_it 2.11 r_mcbond_other 2.11 r_angle_refined_deg 1.516 r_angle_other_deg 0.511 r_chiral_restr 0.067 r_bond_refined_d 0.008 r_gen_planes_refined 0.008 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 3974 Nucleic Acid Atoms Solvent Atoms 353 Heterogen Atoms 38
Software Software Software Name Purpose REFMAC refinement DIALS data reduction Aimless data scaling MOLREP phasing