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Crystal Structure of ProCathepsin L1 from Fasciola hepatica
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1CS8 POLYSERINE MODEL DERIVED FROM PDB ID 1CS8
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 296 0.2M NaSCN, 20% PEG 3350, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 296K
Crystal Properties Matthews coefficient Solvent content 2.13 42.12
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 57.271 α = 90 b = 105.961 β = 90 c = 49.18 γ = 90
Symmetry Space Group P 21 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 ADSC QUANTUM 210 Si 111 Monochromator 2004-01-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 8.3.1 1.11588 ALS 8.3.1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 1.4 57.26 99.7 0.08 14.6 5.6 59595 12.35
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1.4 1.48 98.7 0.549 1.8 2.3
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) 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 POLYSERINE MODEL DERIVED FROM PDB ID 1CS8 1.4 52.93 55989 56141 2985 99.7 0.129 0.128 0.1413 0.165 0.1724 RANDOM 14.07
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] -0.1 0.04 0.07
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.105 r_dihedral_angle_4_deg 18.535 r_dihedral_angle_3_deg 13.278 r_sphericity_free 8.345 r_dihedral_angle_1_deg 7.273 r_scangle_it 5.88 r_scbond_it 4.39 r_sphericity_bonded 3.986 r_rigid_bond_restr 3.174 r_mcangle_it 2.9
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.105 r_dihedral_angle_4_deg 18.535 r_dihedral_angle_3_deg 13.278 r_sphericity_free 8.345 r_dihedral_angle_1_deg 7.273 r_scangle_it 5.88 r_scbond_it 4.39 r_sphericity_bonded 3.986 r_rigid_bond_restr 3.174 r_mcangle_it 2.9 r_mcbond_it 2.459 r_angle_refined_deg 1.792 r_angle_other_deg 1.31 r_mcbond_other 0.821 r_symmetry_hbond_refined 0.32 r_nbtor_refined 0.312 r_symmetry_vdw_other 0.309 r_symmetry_vdw_refined 0.272 r_symmetry_hbond_other 0.226 r_nbd_refined 0.224 r_nbd_other 0.201 r_xyhbond_nbd_other 0.185 r_xyhbond_nbd_refined 0.174 r_chiral_restr 0.118 r_nbtor_other 0.093 r_bond_refined_d 0.02 r_gen_planes_refined 0.016 r_bond_other_d 0.002 r_gen_planes_other 0.001 r_metal_ion_refined r_metal_ion_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2433 Nucleic Acid Atoms Solvent Atoms 388 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction Blu-Ice data collection MOSFLM data reduction SCALA data scaling MOLREP phasing