9RXI | pdb_00009rxi

Schistosoma mansoni Cathepsin D1 bound to Nb10C9

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	Other		SmCD1 apo structure (personal communication)
in silico model	Other		Predicted structure of Nb_10C9 generated with NanoBodyBuilder2

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6	293	PEG 3350, 0.1 M PCTP (sodium propionate, sodium cacodylate trihydrate, bis-tris propane), 0.2 M calcium chloride

Crystal Properties
Matthews coefficient	Solvent content
2.3	46.53

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 70.141	α = 90
b = 181.8	β = 92.41
c = 78.854	γ = 90

Symmetry
Space Group	P 1 21 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	293	PIXEL	DECTRIS EIGER2 X 4M		2024-09-08	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE VMXi	0.7749	Diamond	VMXi

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	Rrim I (All)	Rpim I (All)	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	2.59	90.9	100	0.699	0.194	1	6.7	12.1		61228

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.59	2.63	100		7.966	2.202	0.3	1	12.1

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	2.59	90.9	59131	1900	99.73	0.17498	0.17302	0.1781	0.23408	0.2332	RANDOM	49.399

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]
-1.2		0.41	0.28		0.88

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	16.087
r_long_range_B_refined	10.654
r_long_range_B_other	10.654
r_dihedral_angle_1_deg	8.475
r_scangle_other	7.806
r_dihedral_angle_2_deg	7.601
r_mcangle_it	6.877
r_mcangle_other	6.877
r_scbond_it	4.876
r_scbond_other	4.876
r_mcbond_it	4.405
r_mcbond_other	4.402
r_angle_refined_deg	1.682
r_angle_other_deg	0.55
r_chiral_restr	0.075
r_bond_refined_d	0.007
r_gen_planes_refined	0.006
r_bond_other_d	0.001
r_gen_planes_other	0.001
r_dihedral_angle_4_deg
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	13273
Nucleic Acid Atoms
Solvent Atoms	53
Heterogen Atoms	6

Software

Software
Software Name	Purpose
REFMAC	refinement
DIALS	data scaling
xia2	data reduction
PHASER	phasing
PDB_EXTRACT	data extraction