9FZV | pdb_00009fzv

Structure of cathepsin B1 from Schistosoma mansoni (SmCB1) in complex with a carborane inhibitor

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4I07

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.2	293	200 mM ammonium acetate, 100 mM sodium citrate, 30% PEG 1 500, 2 mM 2-mercaptoethanol, pH 6.2 c (protein)= 5 mg/mL ratio protein:reservoir = 1:1 cryocooled in reservoir solution supplemented with 30% PEG 300, 1.75 mM DTT, 0.07 mM carborane inhibitor 2-oC

Crystal Properties
Matthews coefficient	Solvent content
2.31	46.67

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 81.726	α = 90
b = 81.726	β = 90
c = 102.091	γ = 120

Symmetry
Space Group	P 31

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	PIXEL	DECTRIS PILATUS 6M		2019-04-17	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	BESSY BEAMLINE 14.1	0.918	BESSY	14.1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	CC (Half)	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	2.2	50	99.8	0.985	5.21	5.861		38651

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.2	2.33			0.352

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	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	MOLECULAR REPLACEMENT	THROUGHOUT	2.2	41.4	36677	1972	99.8	0.2044	0.20195	0.2047	0.25024	0.2519	RANDOM	38.734

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]
11.13			11.13		-22.26

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	29.12
r_dihedral_angle_4_deg	19.206
r_dihedral_angle_3_deg	13
r_long_range_B_refined	6.594
r_long_range_B_other	6.594
r_dihedral_angle_1_deg	5.896
r_scangle_other	4.835
r_mcangle_it	4.469
r_mcangle_other	4.469
r_angle_other_deg	3.375
r_scbond_it	3.32
r_scbond_other	3.32
r_mcbond_it	3.179
r_mcbond_other	3.175
r_angle_refined_deg	1.445
r_chiral_restr	0.088
r_bond_refined_d	0.013
r_bond_other_d	0.012
r_gen_planes_refined	0.007
r_gen_planes_other	0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5994
Nucleic Acid Atoms
Solvent Atoms	117
Heterogen Atoms	122

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling
MOLREP	phasing