3S3R

Structure of cathepsin B1 from Schistosoma mansoni in complex with K11777 inhibitor


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.2293reservoir: 0.2 M Ammonium Acetate pH6.2, 0.1 M Na Citrate, 30% PEG 1500, protein buffer and concentration: 10 mM Na-acetate pH 5.5, Cpr = 6 mg/ml, protein: reservoir = 1:1, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.3647.8

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 77.633α = 90
b = 103.121β = 90
c = 100.697γ = 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
12.55099.80.06221.76242662421869.1
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)
12.52.6599.50.6691.855.61184

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 DIFFRACTIONFOURIER SYNTHESISTHROUGHOUTPDB ENTRY 3QSD2.6436.322318722916123698.830.208150.204620.27142RANDOM41.508
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]
-0.220.59-0.38
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.74
r_dihedral_angle_4_deg21.363
r_dihedral_angle_3_deg17.835
r_dihedral_angle_1_deg5.878
r_scangle_it1.491
r_angle_refined_deg1.287
r_scbond_it0.937
r_mcangle_it0.588
r_mcbond_it0.348
r_nbtor_refined0.309
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.74
r_dihedral_angle_4_deg21.363
r_dihedral_angle_3_deg17.835
r_dihedral_angle_1_deg5.878
r_scangle_it1.491
r_angle_refined_deg1.287
r_scbond_it0.937
r_mcangle_it0.588
r_mcbond_it0.348
r_nbtor_refined0.309
r_nbd_refined0.218
r_symmetry_vdw_refined0.198
r_xyhbond_nbd_refined0.143
r_symmetry_hbond_refined0.139
r_chiral_restr0.092
r_bond_refined_d0.011
r_gen_planes_refined0.004
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 Atoms5953
Nucleic Acid Atoms
Solvent Atoms66
Heterogen Atoms123

Software

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