3S3Q

Structure of cathepsin B1 from Schistosoma mansoni in complex with K11017 inhibitor


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3QSDPDB ENTRY 3QSD

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.2293reservoir: 0.2 M Ammonium acetate pH 6.2, 0.1 M Na citrate, 30%(v/w) PEG 1500, protein buffer and concentration: 10 mM Na acetate, pH 5.5, Cpr = 2.5 mg/ml, protein: reservoir: 1:1, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.0840.96

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 33.092α = 90
b = 79.528β = 90
c = 90.269γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 210rmirrors2009-10-16MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 19-BM0.9791APS19-BM

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
11.85099.80.10518.46.8229402289413.2
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)
11.81.83980.4792.33.71134

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 (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONFOURIER SYNTHESISTHROUGHOUTPDB ENTRY 3QSD1.829.842174421548116299.210.1760.169580.166140.23624RANDOM14.087
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]
-0.18-0.070.25
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.337
r_dihedral_angle_4_deg15.311
r_dihedral_angle_3_deg12.42
r_dihedral_angle_1_deg5.816
r_scangle_it2.604
r_scbond_it1.74
r_angle_refined_deg1.268
r_mcangle_it0.976
r_mcbond_it0.642
r_nbtor_refined0.311
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.337
r_dihedral_angle_4_deg15.311
r_dihedral_angle_3_deg12.42
r_dihedral_angle_1_deg5.816
r_scangle_it2.604
r_scbond_it1.74
r_angle_refined_deg1.268
r_mcangle_it0.976
r_mcbond_it0.642
r_nbtor_refined0.311
r_nbd_refined0.215
r_symmetry_hbond_refined0.184
r_symmetry_vdw_refined0.172
r_xyhbond_nbd_refined0.153
r_chiral_restr0.094
r_bond_refined_d0.012
r_gen_planes_refined0.005
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_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1998
Nucleic Acid Atoms
Solvent Atoms536
Heterogen Atoms45

Software

Software
Software NamePurpose
HKL-3000data collection
REFMACrefinement
HKL-3000data reduction
HKL-3000data scaling
REFMACphasing