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The 3.0 A Resolution Structure of Caseinolytic Clp Protease 1 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 5.2 5 MG/ML PROTEIN, 100 MM TRI-NA-CITRATE, PH 5.2, 3% PEG 4000
Crystal Properties Matthews coefficient Solvent content 2.97 58.21
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 96.719 α = 90 b = 168.218 β = 114.6 c = 103.761 γ = 90
Symmetry Space Group P 1 21 1
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 2005-03-07 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 3 59.4 100 0.1 5.9 3.8 60193 2
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 3 3.16 100 0.4
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 3 19.87 57087 3036 100 0.214 0.213 0.2155 0.238 0.2369 RANDOM 14.94
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] 0.34 -0.1 -0.31 -0.12
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.586 r_dihedral_angle_4_deg 27.437 r_dihedral_angle_3_deg 20.549 r_dihedral_angle_1_deg 6.316 r_scangle_it 1.692 r_angle_refined_deg 1.447 r_scbond_it 0.971 r_mcangle_it 0.576 r_symmetry_vdw_refined 0.395 r_mcbond_it 0.379
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.586 r_dihedral_angle_4_deg 27.437 r_dihedral_angle_3_deg 20.549 r_dihedral_angle_1_deg 6.316 r_scangle_it 1.692 r_angle_refined_deg 1.447 r_scbond_it 0.971 r_mcangle_it 0.576 r_symmetry_vdw_refined 0.395 r_mcbond_it 0.379 r_symmetry_hbond_refined 0.341 r_nbtor_refined 0.32 r_nbd_refined 0.233 r_xyhbond_nbd_refined 0.124 r_chiral_restr 0.089 r_bond_refined_d 0.014 r_gen_planes_refined 0.004 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 18482 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling MOLREP phasing