3QSD | pdb_00003qsd

Structure of cathepsin B1 from Schistosoma mansoni in complex with CA074 inhibitor

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1HUC

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.1	293	0.2M Ammonium Acetate, 0.1M Na Citrate, 30% (v/w) PEG 1500, 10mM Na Acetate pH 5.5, Cpr concentration = 5 mg/ml protein:reservoir - 1:1 , VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.09	41.06

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 33.177	α = 90
b = 79.16	β = 90
c = 90.61	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	1.3	50	93.5	0.053	26.29	5.5	59635	55759			8.5

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	61.6		0.281	2.7	3.1

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	1HUC	1.3	22.33	56435	52880	2805	93.57	0.11608	0.11608	0.11407	0.12	0.15473	0.16	RANDOM	12.333

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]
-0.28			0.11		0.17

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.161
r_dihedral_angle_4_deg	13.296
r_dihedral_angle_3_deg	12.012
r_sphericity_free	10.028
r_dihedral_angle_1_deg	5.967
r_sphericity_bonded	5.028
r_scangle_it	4.501
r_scbond_it	3.404
r_mcangle_it	2.679
r_rigid_bond_restr	2.033
r_mcbond_it	2.019
r_angle_refined_deg	1.808
r_nbtor_refined	0.318
r_symmetry_hbond_refined	0.293
r_symmetry_vdw_refined	0.275
r_nbd_refined	0.241
r_xyhbond_nbd_refined	0.182
r_chiral_restr	0.12
r_bond_refined_d	0.018
r_gen_planes_refined	0.013
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	1991
Nucleic Acid Atoms
Solvent Atoms	472
Heterogen Atoms	42

Software

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