3S3R | pdb_00003s3r

Structure of cathepsin B1 from Schistosoma mansoni in complex with K11777 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 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 coefficient	Solvent content
2.36	47.8

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 77.633	α = 90
b = 103.121	β = 90
c = 100.697	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	2.5	50	99.8	0.062	21.7	6	24266	24218			69.1

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	2.5	2.65	99.5		0.669	1.85	5.6	1184

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 (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	FOURIER SYNTHESIS	THROUGHOUT	PDB ENTRY 3QSD	2.64	36.32	23187	22916	1236	98.83	0.20815	0.20462	0.2	0.27142	0.27	RANDOM	41.508

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]
-0.22			0.59		-0.38

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.74
r_dihedral_angle_4_deg	21.363
r_dihedral_angle_3_deg	17.835
r_dihedral_angle_1_deg	5.878
r_scangle_it	1.491
r_angle_refined_deg	1.287
r_scbond_it	0.937
r_mcangle_it	0.588
r_mcbond_it	0.348
r_nbtor_refined	0.309
r_nbd_refined	0.218
r_symmetry_vdw_refined	0.198
r_xyhbond_nbd_refined	0.143
r_symmetry_hbond_refined	0.139
r_chiral_restr	0.092
r_bond_refined_d	0.011
r_gen_planes_refined	0.004
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 Atoms	Number
Protein Atoms	5953
Nucleic Acid Atoms
Solvent Atoms	66
Heterogen Atoms	123

Software

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