4I05

Structure of intermediate processing form of cathepsin B1 from Schistosoma mansoni

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5.6	293	Reservoir: 0.2M Ammonium Acetate, 0.1M Sodium Citrate, 30% PEG 4000. Protein buffer and concentration: 5mM Sodium Acetate, pH 5.5, Cpr=1.5mg/ml. Ratio Protein: Reservoir=1:0.75. Cryocooled in mother liquor., VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.32	46.89

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 93.859	α = 90
b = 50.988	β = 91.31
c = 62.546	γ = 90

Symmetry
Space Group	C 1 2 1

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	2008-07-10	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 19-BM	0.979	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	1.9	50	99.4	0.082	18.2	3	23701	23559

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.9	1.93	98.7		0.35	0.0313		2.7

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	3QSD	1.9	25.52	22581	22107	1201	99.29	0.16587	0.16308	0.21642	RANDOM	23.249

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		0.02	-0.22		0.04

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.147
r_dihedral_angle_4_deg	17.076
r_dihedral_angle_3_deg	13.899
r_dihedral_angle_1_deg	5.814
r_scangle_it	2.668
r_scbond_it	1.661
r_angle_refined_deg	1.487
r_mcangle_it	0.897
r_mcbond_it	0.512
r_nbtor_refined	0.303
r_nbd_refined	0.198
r_symmetry_vdw_refined	0.195
r_xyhbond_nbd_refined	0.146
r_symmetry_hbond_refined	0.137
r_chiral_restr	0.109
r_bond_refined_d	0.013
r_gen_planes_refined	0.008
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	2199
Nucleic Acid Atoms
Solvent Atoms	340
Heterogen Atoms	1

Software

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