☰ Navigation Tabs
Crystal structure of Wild-Type Mycobacterium tuberculosis ClpC1 N-terminal domain in complex with Lassomycin
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3WDB
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 291 1.4 M sodium acetate,
0.1 M sodium cacodylate (pH 6.5)
Crystal Properties Matthews coefficient Solvent content 2.57 52.14
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 47.431 α = 90 b = 58.468 β = 90 c = 64.763 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 103 CCD MARMOSAIC 225 mm CCD 2019-09-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON RRCAT INDUS-2 BEAMLINE PX-BL21 0.9794 RRCAT INDUS-2 PX-BL21
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.83 36.86 100 0.038 30.4 7.6 16474
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.83 1.87 0.497 4
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 1.83 36.86 15605 821 99.9 0.185 0.183 0.194 0.236 0.2444 RANDOM 35.99
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] 2.36 -1.18 -1.18
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.734 r_dihedral_angle_4_deg 17.836 r_dihedral_angle_3_deg 13.781 r_long_range_B_other 9.157 r_long_range_B_refined 9.152 r_scangle_other 7.247 r_dihedral_angle_1_deg 6.441 r_scbond_it 5.323 r_scbond_other 5.319 r_mcangle_it 4.867
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.734 r_dihedral_angle_4_deg 17.836 r_dihedral_angle_3_deg 13.781 r_long_range_B_other 9.157 r_long_range_B_refined 9.152 r_scangle_other 7.247 r_dihedral_angle_1_deg 6.441 r_scbond_it 5.323 r_scbond_other 5.319 r_mcangle_it 4.867 r_mcangle_other 4.864 r_mcbond_it 3.877 r_mcbond_other 3.832 r_angle_refined_deg 1.546 r_angle_other_deg 1.226 r_chiral_restr 0.097 r_bond_refined_d 0.013 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 1236 Nucleic Acid Atoms Solvent Atoms 57 Heterogen Atoms 8
Software Software Software Name Purpose REFMAC refinement iMOSFLM data reduction Aimless data scaling MOLREP phasing