4I04 | pdb_00004i04

Structure of zymogen 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	6	293	Reservoir: 0.1M Ammonium Acetate, 0.1M Bis-Tris, 17% PEG 10000. Protein buffer and concentration: 5mM Sodium Acetate, pH 5.5, Cpr=5.25mg/ml. Ratio Protein: Reservoir=2:1. Cryocooled in mother liquor containing 20% ethylene glycol., VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.4	48.65

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 54.281	α = 76.97
b = 83.172	β = 86.6
c = 84.569	γ = 71.11

Symmetry
Space Group	P 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	MARMOSAIC 225 mm CCD	Double crystal monochromator with 2 sets of Rh-soated silicon and glass mirrors	2011-06-01	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	BESSY BEAMLINE 14.2	0.914	BESSY	14.2

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	1.95	50	78.4	0.037	25.9	2.3		78650			25.2

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	1.95	1.98	42.1		0.296	3.1	1.9

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	3QSD	1.95	38.4	95142	71614	3756	75.27	0.20195	0.20195	0.19927	0.2	0.25245	0.25	RANDOM	21.792

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]
	0.01	0.01	0.01	0.01	-0.01

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.195
r_dihedral_angle_4_deg	17.278
r_dihedral_angle_3_deg	15.521
r_dihedral_angle_1_deg	6.062
r_scangle_it	2.26
r_scbond_it	1.513
r_angle_refined_deg	1.303
r_mcangle_it	0.911
r_mcbond_it	0.565
r_nbtor_refined	0.306
r_symmetry_hbond_refined	0.227
r_nbd_refined	0.205
r_symmetry_vdw_refined	0.181
r_xyhbond_nbd_refined	0.151
r_chiral_restr	0.098
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	9797
Nucleic Acid Atoms
Solvent Atoms	519
Heterogen Atoms	24

Software

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