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Structure of E166A BlaC from Mycobacterium tuberculosis at pH 4.5
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 4.5 293 0.05 M LiSO4 (Salt)
0.1 M Na Acet 4.5 pH (Buffer)
25 %w/v PEG 8K (Precipitant)
Crystal Properties Matthews coefficient Solvent content 2.03 39.38
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 38.955 α = 90 b = 54.745 β = 92.89 c = 53.759 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 PILATUS3 2M 2023-04-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE MASSIF-1 0.8731 ESRF MASSIF-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 1.42 54.74 99.3 0.161 0.853 8 1.4 42647
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 1.42 1.44 96 0.575
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 1.42 38.36 40243 2384 99.26 0.19023 0.18897 0.1955 0.21056 0.2 RANDOM 15.809
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] 2.02 0.73 -0.06 -2.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 12.415 r_dihedral_angle_2_deg 8.178 r_dihedral_angle_1_deg 6.407 r_long_range_B_refined 4.672 r_long_range_B_other 4.365 r_scangle_other 3.082 r_scbond_it 2.213 r_scbond_other 2.088 r_mcangle_it 1.929 r_mcangle_other 1.928
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 12.415 r_dihedral_angle_2_deg 8.178 r_dihedral_angle_1_deg 6.407 r_long_range_B_refined 4.672 r_long_range_B_other 4.365 r_scangle_other 3.082 r_scbond_it 2.213 r_scbond_other 2.088 r_mcangle_it 1.929 r_mcangle_other 1.928 r_angle_refined_deg 1.466 r_mcbond_it 1.344 r_mcbond_other 1.344 r_angle_other_deg 0.514 r_chiral_restr 0.075 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 1985 Nucleic Acid Atoms Solvent Atoms 241 Heterogen Atoms 10
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling MOLREP phasing