3F75

Activated Toxoplasma gondii cathepsin L (TgCPL) in complex with its propeptide


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1CS8PDB entry 1CS8 (protease domain only)

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP429840% 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 coefficientSolvent content
2.1743.21

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 65.621α = 90
b = 65.621β = 90
c = 149.772γ = 90
Symmetry
Space GroupP 43 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 325 mm CCD2008-03-19MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRL BEAMLINE BL11-10.9800SSRLBL11-1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge 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
11.995099.90.12218.1288.7232662326625
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.992.0699.20.7442.88.52242

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB entry 1CS8 (protease domain only)1.9933.9823178118699.890.167390.165380.20557RANDOM16.904
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]
0.720.72-1.43
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.752
r_dihedral_angle_4_deg14.757
r_dihedral_angle_3_deg12.772
r_dihedral_angle_1_deg5.542
r_scangle_it4.958
r_scbond_it3.299
r_mcangle_it2.581
r_mcbond_it1.695
r_angle_other_deg1.187
r_angle_refined_deg1.156
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.752
r_dihedral_angle_4_deg14.757
r_dihedral_angle_3_deg12.772
r_dihedral_angle_1_deg5.542
r_scangle_it4.958
r_scbond_it3.299
r_mcangle_it2.581
r_mcbond_it1.695
r_angle_other_deg1.187
r_angle_refined_deg1.156
r_mcbond_other0.541
r_chiral_restr0.07
r_bond_refined_d0.01
r_gen_planes_refined0.005
r_bond_other_d0.001
r_gen_planes_other0.001
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 AtomsNumber
Protein Atoms2345
Nucleic Acid Atoms
Solvent Atoms165
Heterogen Atoms7

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
Blu-Icedata collection
HKL-2000data reduction
HKL-2000data scaling