☰ Navigation Tabs
Structure of G132N 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 6.5 293 0.1 M MES, 0.1 M Imidazole, 0.09 M Halogens (Sodium Bromide, Sodium Iodide, Sodium Fluoride), 30% w/v EDO P8K mix(Ethylene Glycol, PEG 8000)
Crystal Properties Matthews coefficient Solvent content 2.06 40.36
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 54.007 α = 90 b = 54.596 β = 90 c = 79.398 γ = 90
Symmetry Space Group P 21 21 21
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 PILATUS 6M-F 2020-02-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 0.912 Diamond I04-1
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 1.6 45.03 99 0.056 0.997 6 1.8 31258
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.6 1.63 0.63 1.5 1.8
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 1.6 45.03 29653 1560 98.58 0.15682 0.1552 0.1702 0.18785 0.1999 RANDOM 14.978
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] -0.45 -0.55 1
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.41 r_dihedral_angle_4_deg 19.446 r_dihedral_angle_3_deg 11.342 r_dihedral_angle_1_deg 6.351 r_long_range_B_refined 4.818 r_long_range_B_other 4.817 r_scangle_other 3.013 r_scbond_it 2.104 r_scbond_other 2.103 r_mcangle_other 1.857
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.41 r_dihedral_angle_4_deg 19.446 r_dihedral_angle_3_deg 11.342 r_dihedral_angle_1_deg 6.351 r_long_range_B_refined 4.818 r_long_range_B_other 4.817 r_scangle_other 3.013 r_scbond_it 2.104 r_scbond_other 2.103 r_mcangle_other 1.857 r_mcangle_it 1.853 r_angle_refined_deg 1.448 r_mcbond_it 1.204 r_angle_other_deg 1.201 r_mcbond_other 1.195 r_chiral_restr 0.089 r_bond_refined_d 0.01 r_gen_planes_refined 0.006 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_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2004 Nucleic Acid Atoms Solvent Atoms 165 Heterogen Atoms 87
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling MOLREP phasing