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Structure of S70A BlaC from Mycobacterium tuberculosis obtained from crystals produced in the presence of DTT
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 Tris-HCl, pH 7.0
1.7 M NH4H2PO4
Crystal Properties Matthews coefficient Solvent content 4.35 71.73
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 108.864 α = 90 b = 108.864 β = 90 c = 260.577 γ = 90
Symmetry Space Group P 43 21 2
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 R 4M 2016-11-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID30B 0.9677 ESRF ID30B
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 2.54 49.73 99.9 0.034 0.999 18.9 13.6 714649
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 2.54 2.63 99.9 0.49 0.701 1.7 14.1
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 2.54 49.73 49780 2628 99.62 0.22945 0.228 0.2327 0.25634 0.2585 RANDOM 63.052
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] 2.1 2.1 -4.19
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.543 r_dihedral_angle_4_deg 20.006 r_dihedral_angle_3_deg 15.979 r_long_range_B_refined 9.707 r_long_range_B_other 9.706 r_scangle_other 8.234 r_mcangle_it 6.966 r_mcangle_other 6.965 r_dihedral_angle_1_deg 6.616 r_scbond_it 6.003
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.543 r_dihedral_angle_4_deg 20.006 r_dihedral_angle_3_deg 15.979 r_long_range_B_refined 9.707 r_long_range_B_other 9.706 r_scangle_other 8.234 r_mcangle_it 6.966 r_mcangle_other 6.965 r_dihedral_angle_1_deg 6.616 r_scbond_it 6.003 r_scbond_other 6.002 r_mcbond_it 5.161 r_mcbond_other 5.145 r_angle_refined_deg 1.757 r_angle_other_deg 1.082 r_chiral_restr 0.101 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 5885 Nucleic Acid Atoms Solvent Atoms 53 Heterogen Atoms 108
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling MOLREP phasing