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Crystal structure 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 293 0.1 M sodium acetate pH 5.0, 25% PEG1500
Crystal Properties Matthews coefficient Solvent content 2.06 40.36
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 39.589 α = 104.29 b = 41.417 β = 90.07 c = 76.523 γ = 90.67
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 2015-10-31 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE MASSIF-1 0.96773 ESRF MASSIF-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) 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 1.93 40.13 94.2 0.09 0.074 6.8 2.2 33346
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.93 2 81.4 0.586 0.572 1.3 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 2.1 40.13 25143 1317 96.22 0.20803 0.20574 0.2158 0.25043 0.2535 RANDOM 19.828
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] -1.86 0.57 0.04 2.92 0.37 -1.12
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.293 r_dihedral_angle_4_deg 19.472 r_dihedral_angle_3_deg 13.08 r_dihedral_angle_1_deg 6.713 r_long_range_B_other 3.637 r_long_range_B_refined 3.636 r_mcangle_it 2.252 r_mcangle_other 2.252 r_scangle_other 2.226 r_angle_refined_deg 1.658
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.293 r_dihedral_angle_4_deg 19.472 r_dihedral_angle_3_deg 13.08 r_dihedral_angle_1_deg 6.713 r_long_range_B_other 3.637 r_long_range_B_refined 3.636 r_mcangle_it 2.252 r_mcangle_other 2.252 r_scangle_other 2.226 r_angle_refined_deg 1.658 r_scbond_it 1.495 r_scbond_other 1.492 r_mcbond_it 1.49 r_mcbond_other 1.468 r_angle_other_deg 1.013 r_chiral_restr 0.088 r_bond_refined_d 0.014 r_gen_planes_refined 0.007 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 4030 Nucleic Acid Atoms Solvent Atoms 135 Heterogen Atoms 59
Software Software Software Name Purpose REFMAC refinement MOLREP phasing