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Crystal structure of A55E 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 7.5 293 0.8 M Disodium Succinate
Crystal Properties Matthews coefficient Solvent content 2 38.59
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 38.99 α = 90 b = 54.356 β = 91.94 c = 53.687 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 EIGER X 16M 2019-06-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06SA 1.000 SLS X06SA
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 1.4 38.21 96.9 0.078 0.985 5.2 2.5 42718
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 1.4 1.42 94.2 0.344 0.752 2.3
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 2GDN 1.4 38.21 40621 2079 96.53 0.14896 0.14758 0.1477 0.17725 0.1779 RANDOM 9.519
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] 0.19 0.23 0.41 -0.61
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.651 r_dihedral_angle_4_deg 19.402 r_dihedral_angle_3_deg 11.336 r_dihedral_angle_1_deg 6.813 r_rigid_bond_restr 4.814 r_long_range_B_refined 1.866 r_angle_refined_deg 1.781 r_long_range_B_other 1.765 r_angle_other_deg 1.637 r_scangle_other 1.453
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.651 r_dihedral_angle_4_deg 19.402 r_dihedral_angle_3_deg 11.336 r_dihedral_angle_1_deg 6.813 r_rigid_bond_restr 4.814 r_long_range_B_refined 1.866 r_angle_refined_deg 1.781 r_long_range_B_other 1.765 r_angle_other_deg 1.637 r_scangle_other 1.453 r_scbond_it 1.285 r_scbond_other 1.262 r_mcangle_it 0.888 r_mcangle_other 0.888 r_mcbond_it 0.648 r_mcbond_other 0.642 r_chiral_restr 0.098 r_bond_refined_d 0.014 r_gen_planes_refined 0.011 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 1996 Nucleic Acid Atoms Solvent Atoms 207 Heterogen Atoms 59
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling MOLREP phasing