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Activated Toxoplasma gondii cathepsin L (TgCPL) in complex with its propeptide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1CS8 PDB entry 1CS8 (protease domain only)
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 4 298 40% PEG 8000, 0.1M Ammonium bromide, 0.1M Sodium citrate pH 4.0. Cryoprotected with ~10% Ethylene glycol, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.17 43.21
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 65.621 α = 90 b = 65.621 β = 90 c = 149.772 γ = 90
Symmetry Space Group P 43 21 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD MARMOSAIC 325 mm CCD 2008-03-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL11-1 0.9800 SSRL BL11-1
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 1.99 50 99.9 0.122 18.128 8.7 23266 23266 25
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 1.99 2.06 99.2 0.744 2.8 8.5 2242
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 1CS8 (protease domain only) 1.99 33.98 23178 1186 99.89 0.16739 0.16538 0.1783 0.20557 0.2185 RANDOM 16.904
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] 0.72 0.72 -1.43
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.752 r_dihedral_angle_4_deg 14.757 r_dihedral_angle_3_deg 12.772 r_dihedral_angle_1_deg 5.542 r_scangle_it 4.958 r_scbond_it 3.299 r_mcangle_it 2.581 r_mcbond_it 1.695 r_angle_other_deg 1.187 r_angle_refined_deg 1.156
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.752 r_dihedral_angle_4_deg 14.757 r_dihedral_angle_3_deg 12.772 r_dihedral_angle_1_deg 5.542 r_scangle_it 4.958 r_scbond_it 3.299 r_mcangle_it 2.581 r_mcbond_it 1.695 r_angle_other_deg 1.187 r_angle_refined_deg 1.156 r_mcbond_other 0.541 r_chiral_restr 0.07 r_bond_refined_d 0.01 r_gen_planes_refined 0.005 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_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2345 Nucleic Acid Atoms Solvent Atoms 165 Heterogen Atoms 7
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction Blu-Ice data collection HKL-2000 data reduction HKL-2000 data scaling