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Crystal structure of I105Y/S130G double mutant of BlaC from Mycobacterium tuberculosis
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 4.5 291 0.015M Zn Chloride, 0.13M Na Acetate, 22%v/v PEGSM
Crystal Properties Matthews coefficient Solvent content 1.94 36.67
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 39.44 α = 90 b = 41.425 β = 90 c = 269.624 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 EIGER2 S 9M 2023-06-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID30B 0.8731 ESRF ID30B
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 1.3 135.18 99.7 0.972 12.2 1.9 109981
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 1.3 1.32 0.79
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 1.3 135.18 104543 5438 99.68 0.14206 0.14041 0.1444 0.17407 0.1818 RANDOM 13.381
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] -0.52 0.12 0.4
RMS Deviations Key Refinement Restraint Deviation r_long_range_B_refined 11.178 r_dihedral_angle_3_deg 11.099 r_long_range_B_other 10.021 r_dihedral_angle_2_deg 8.414 r_dihedral_angle_1_deg 6.648 r_scangle_other 4.047 r_rigid_bond_restr 3.039 r_mcangle_other 2.853 r_mcangle_it 2.852 r_scbond_it 2.76
RMS Deviations Key Refinement Restraint Deviation r_long_range_B_refined 11.178 r_dihedral_angle_3_deg 11.099 r_long_range_B_other 10.021 r_dihedral_angle_2_deg 8.414 r_dihedral_angle_1_deg 6.648 r_scangle_other 4.047 r_rigid_bond_restr 3.039 r_mcangle_other 2.853 r_mcangle_it 2.852 r_scbond_it 2.76 r_scbond_other 2.759 r_mcbond_it 1.899 r_mcbond_other 1.876 r_angle_refined_deg 1.864 r_angle_other_deg 0.653 r_chiral_restr 0.1 r_bond_refined_d 0.01 r_gen_planes_refined 0.01 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_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3990 Nucleic Acid Atoms Solvent Atoms 694 Heterogen Atoms 15
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling MOLREP phasing