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Crystal structure of BlaC from Mycobacterium tuberculosis bound to phosphate
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 293.15 0.1 M sodium acetate buffer, pH 5.0, 25% PEG1500
Crystal Properties Matthews coefficient Solvent content 2.15 42.88
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 39.591 α = 101.28 b = 41.683 β = 90.11 c = 76.841 γ = 90.43
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 4M 2016-11-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE MASSIF-3 0.9677 ESRF MASSIF-3
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 1.19 75.36 62.7 0.063 0.041 0.998 11.3 3.2 96841
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.19 1.23 0.573 0.467 0.523 1.2 2
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 1.19 75.36 92053 4773 62.69 0.16797 0.16683 0.1763 0.18953 0.1953 RANDOM 11.803
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] -0.32 0.32 0.03 0.71 -0.01 -0.37
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.498 r_dihedral_angle_4_deg 21.668 r_dihedral_angle_3_deg 11.445 r_dihedral_angle_1_deg 6.294 r_long_range_B_refined 3.833 r_long_range_B_other 3.833 r_scangle_other 3.137 r_scbond_it 2.234 r_scbond_other 2.234 r_angle_refined_deg 2.185
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.498 r_dihedral_angle_4_deg 21.668 r_dihedral_angle_3_deg 11.445 r_dihedral_angle_1_deg 6.294 r_long_range_B_refined 3.833 r_long_range_B_other 3.833 r_scangle_other 3.137 r_scbond_it 2.234 r_scbond_other 2.234 r_angle_refined_deg 2.185 r_mcangle_other 1.935 r_mcangle_it 1.933 r_mcbond_it 1.315 r_mcbond_other 1.299 r_angle_other_deg 1.124 r_chiral_restr 0.153 r_bond_refined_d 0.021 r_gen_planes_refined 0.012 r_bond_other_d 0.002 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_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4045 Nucleic Acid Atoms Solvent Atoms 288 Heterogen Atoms 60
Software Software Software Name Purpose REFMAC refinement