4I07 | pdb_00004i07

Structure of mature 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=2.5mg/ml. Ratio Protein: Reservoir=1:1. Cryocooled in mother liquor, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.08	40.86

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 33.143	α = 90
b = 79.173	β = 90
c = 90.483	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	2008-07-10	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 19-BM	0.978	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	1.3	50	89.9	0.077	33.7	7.3	66361	59658			13.5

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	1.3	1.32	49.3		0.438	4	5.7

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 (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	1.3	19.79	56496	50812	2711	89.95	0.13936	0.13936	0.1374	0.14	0.17667	0.18	RANDOM	11.512

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]
0.52			-0.39		-0.13

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.279
r_dihedral_angle_4_deg	13.942
r_dihedral_angle_3_deg	11.924
r_sphericity_free	6.247
r_dihedral_angle_1_deg	5.799
r_sphericity_bonded	4.449
r_scangle_it	3.857
r_scbond_it	2.718
r_mcangle_it	2.096
r_rigid_bond_restr	1.537
r_mcbond_it	1.473
r_angle_refined_deg	1.437
r_nbtor_refined	0.311
r_symmetry_vdw_refined	0.204
r_nbd_refined	0.201
r_xyhbond_nbd_refined	0.191
r_symmetry_hbond_refined	0.15
r_chiral_restr	0.098
r_bond_refined_d	0.013
r_gen_planes_refined	0.009
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

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1993
Nucleic Acid Atoms
Solvent Atoms	427
Heterogen Atoms	5

Software

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