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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 2CBY PDB ENTRY 2CBY
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 THE PROTEIN WAS CRYSTALLIZED BY THE SITTING DROP METHOD WITH 400NL PROTEIN PLUS 400NL MOTHERLIQUOR AND 100UL RESERVOIR. CONDITION WAS IDENTIFIED USING A SET OF RANDOM CONDITIONS GENERATED WITH CRYSTOOL SOFTWARE AND OPTIMIZED TO 9.576% (W/V) PEG 2000 0.2M LITHIUM SULFATE 0.1M MOPS (4-MORPHOLINEPROPANESULFONIC ACID) PH 6.5 WITH CRYSTOOL BY REDUCING THE PARAMETER SPACE TO THE REAGENTS UTILIZED. CRYSTALS SHOWED AFTER 2 DAYS
Crystal Properties Matthews coefficient Solvent content 2.32 47
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 97.719 α = 90 b = 168.948 β = 114.83 c = 104.364 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 77 CCD ADSC CCD 2005-07-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 5.0.2 ALS 5.0.2
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 49.5 100 0.08 10 6 90593 61.1
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 2.69 86 0.45 1.7 3.8
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 PDB ENTRY 2CBY 2.6 169.03 90592 4542 95.7 0.205 0.202 0.1954 0.261 0.2513 RANDOM 29.23
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] 6.669 -0.409 -5.613 -1.399
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.112 r_dihedral_angle_3_deg 20.183 r_dihedral_angle_4_deg 18.126 r_dihedral_angle_1_deg 6.324 r_scangle_it 2.405 r_scbond_it 1.494 r_angle_refined_deg 1.387 r_mcangle_it 0.95 r_mcbond_it 0.552 r_nbtor_refined 0.313
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.112 r_dihedral_angle_3_deg 20.183 r_dihedral_angle_4_deg 18.126 r_dihedral_angle_1_deg 6.324 r_scangle_it 2.405 r_scbond_it 1.494 r_angle_refined_deg 1.387 r_mcangle_it 0.95 r_mcbond_it 0.552 r_nbtor_refined 0.313 r_nbd_refined 0.22 r_symmetry_vdw_refined 0.203 r_symmetry_hbond_refined 0.194 r_xyhbond_nbd_refined 0.131 r_chiral_restr 0.091 r_bond_refined_d 0.012 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 18064 Nucleic Acid Atoms Solvent Atoms 117 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling