2O6X

Crystal Structure of ProCathepsin L1 from Fasciola hepatica


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP72960.2M NaSCN, 20% PEG 3350, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 296K
Crystal Properties
Matthews coefficientSolvent content
2.1342.12

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 57.271α = 90
b = 105.961β = 90
c = 49.18γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 210Si 111 Monochromator2004-01-12MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALS BEAMLINE 8.3.11.11588ALS8.3.1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym I (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
11.457.2699.70.0814.65.65959512.35
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
1.41.4898.70.5491.82.3

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPOLYSERINE MODEL DERIVED FROM PDB ID 1CS81.452.935598956141298599.70.1290.1280.165RANDOM14.07
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]
-0.10.040.07
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.105
r_dihedral_angle_4_deg18.535
r_dihedral_angle_3_deg13.278
r_sphericity_free8.345
r_dihedral_angle_1_deg7.273
r_scangle_it5.88
r_scbond_it4.39
r_sphericity_bonded3.986
r_rigid_bond_restr3.174
r_mcangle_it2.9
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.105
r_dihedral_angle_4_deg18.535
r_dihedral_angle_3_deg13.278
r_sphericity_free8.345
r_dihedral_angle_1_deg7.273
r_scangle_it5.88
r_scbond_it4.39
r_sphericity_bonded3.986
r_rigid_bond_restr3.174
r_mcangle_it2.9
r_mcbond_it2.459
r_angle_refined_deg1.792
r_angle_other_deg1.31
r_mcbond_other0.821
r_symmetry_hbond_refined0.32
r_nbtor_refined0.312
r_symmetry_vdw_other0.309
r_symmetry_vdw_refined0.272
r_symmetry_hbond_other0.226
r_nbd_refined0.224
r_nbd_other0.201
r_xyhbond_nbd_other0.185
r_xyhbond_nbd_refined0.174
r_chiral_restr0.118
r_nbtor_other0.093
r_bond_refined_d0.02
r_gen_planes_refined0.016
r_bond_other_d0.002
r_gen_planes_other0.001
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 AtomsNumber
Protein Atoms2433
Nucleic Acid Atoms
Solvent Atoms388
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
Blu-Icedata collection
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing