3S3Q

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

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3QSD	PDB ENTRY 3QSD

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.2	293	reservoir: 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 coefficient	Solvent content
2.08	40.96

Crystal Data

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

Symmetry
Space Group	P 21 21 21

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 210r	mirrors	2009-10-16	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 19-BM	0.9791	APS	19-BM

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge 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	1.8	50	99.8	0.105	18.4	6.8	22940	22894			13.2

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.8	1.83	98		0.479	2.3	3.7	1134

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 (All)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	FOURIER SYNTHESIS	THROUGHOUT	PDB ENTRY 3QSD	1.8	29.84	21744	21548	1162	99.21	0.176	0.16958	0.16614	0.23624	RANDOM	14.087

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			-0.07		0.25

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.337
r_dihedral_angle_4_deg	15.311
r_dihedral_angle_3_deg	12.42
r_dihedral_angle_1_deg	5.816
r_scangle_it	2.604
r_scbond_it	1.74
r_angle_refined_deg	1.268
r_mcangle_it	0.976
r_mcbond_it	0.642
r_nbtor_refined	0.311
r_nbd_refined	0.215
r_symmetry_hbond_refined	0.184
r_symmetry_vdw_refined	0.172
r_xyhbond_nbd_refined	0.153
r_chiral_restr	0.094
r_bond_refined_d	0.012
r_gen_planes_refined	0.005
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 Atoms	Number
Protein Atoms	1998
Nucleic Acid Atoms
Solvent Atoms	536
Heterogen Atoms	45

Software

Software
Software Name	Purpose
HKL-3000	data collection
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling
REFMAC	phasing