☰ Navigation Tabs
Structure of BlaC from Mycobacterium tuberculosis bound to the trans-enamine adduct derived from clavulanic acid.
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, pH 5.0
25% w/v PEG1500
Crystal Properties Matthews coefficient Solvent content 2.13 42.18
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 39.65 α = 78.4 b = 41.98 β = 89.95 c = 76.917 γ = 89.75
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 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 1.93 41.12 94.4 0.124 0.974 4.4 2.3 34426
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 1.93 2 85.4 0.342 0.709 1.8 2.1
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 1.93 41.12 32697 1723 94.43 0.23054 0.22859 0.2416 0.26694 0.2848 RANDOM 14.358
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] -0.95 0.26 -0.35 2.73 0.37 -1.5
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.399 r_dihedral_angle_4_deg 20.152 r_dihedral_angle_3_deg 14.555 r_dihedral_angle_1_deg 6.185 r_long_range_B_refined 2.903 r_long_range_B_other 2.902 r_angle_refined_deg 1.66 r_scangle_other 1.602 r_mcangle_it 1.443 r_mcangle_other 1.442
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.399 r_dihedral_angle_4_deg 20.152 r_dihedral_angle_3_deg 14.555 r_dihedral_angle_1_deg 6.185 r_long_range_B_refined 2.903 r_long_range_B_other 2.902 r_angle_refined_deg 1.66 r_scangle_other 1.602 r_mcangle_it 1.443 r_mcangle_other 1.442 r_scbond_it 1.026 r_scbond_other 1.026 r_angle_other_deg 1.014 r_mcbond_it 0.892 r_mcbond_other 0.89 r_chiral_restr 0.087 r_bond_refined_d 0.013 r_gen_planes_refined 0.007 r_bond_other_d 0.002 r_gen_planes_other 0.002 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 4018 Nucleic Acid Atoms Solvent Atoms 112 Heterogen Atoms 72
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling MOLREP phasing