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Crystal structure of the ATP-dependent Clp Protease proteolytic subunit 1 (ClpP1) from Mycobacterium tuberculosis
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1TYF PDB ENTRY 1TYF
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 THE PROTEIN WAS CRYSTALLISED BY THE VAPOUR DIFFUSION METHOD IN HANGING DROPS CONTAINING A 1:1 MIXTURE OF 3 MG/ML PROTEIN SOLUTION (IN 50 MM TRIS-HCL PH 8) AND RESERVOIR SOLUTION INCLUDING 1 M AMMONIUM SULPHATE IN 0.1 M HEPES PH 8.
Crystal Properties Matthews coefficient Solvent content 3.83 67.91
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 178.255 α = 90 b = 178.255 β = 90 c = 264.914 γ = 120
Symmetry Space Group P 61 2 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 110 CCD MARRESEARCH 2001-08-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-3 ESRF ID14-3
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 2.6 76.7 100 0.16 24.3 22.2 76728 40.12
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 2.6 2.74 100 0.69 6.6 22.5
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 PDB ENTRY 1TYF 2.6 154.3 76647 3895 100 0.194 0.192 0.1882 0.229 0.2249 RANDOM 19.59
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] 0.872 0.436 0.872 -1.307
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.912 r_dihedral_angle_3_deg 19.468 r_dihedral_angle_4_deg 18.233 r_dihedral_angle_1_deg 6.21 r_scangle_it 3.798 r_scbond_it 2.318 r_angle_refined_deg 1.48 r_mcangle_it 1.333 r_mcbond_it 0.805 r_nbtor_refined 0.313
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.912 r_dihedral_angle_3_deg 19.468 r_dihedral_angle_4_deg 18.233 r_dihedral_angle_1_deg 6.21 r_scangle_it 3.798 r_scbond_it 2.318 r_angle_refined_deg 1.48 r_mcangle_it 1.333 r_mcbond_it 0.805 r_nbtor_refined 0.313 r_nbd_refined 0.216 r_symmetry_vdw_refined 0.193 r_symmetry_hbond_refined 0.188 r_xyhbond_nbd_refined 0.125 r_chiral_restr 0.102 r_bond_refined_d 0.014 r_gen_planes_refined 0.005 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9149 Nucleic Acid Atoms Solvent Atoms 301 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling AMoRE phasing