9HK2 | pdb_00009hk2

Crystal structure of cathepsin D from Schistosoma mansoni

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
in silico model	AlphaFold	G4VEV6

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.5	293.15	0.1 M Tris-HCl buffer pH 7,5 0.2M Li2SO4 25% PEG3350 The crystallization drop was composed of 2 ul protein solution + 0.8 ul precipitant solution + 0.2 ul seed stock.

Crystal Properties
Matthews coefficient	Solvent content
2.68	54.11

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 202.485	α = 90
b = 202.485	β = 90
c = 104.271	γ = 120

Symmetry
Space Group	H 3 2

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 300K		2020-12-14	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	BESSY BEAMLINE 14.2	0.9184	BESSY	14.2

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (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	3.2	44.852	100	0.535	0.589	0.244	0.974	9.3	11.1		13135			67.32

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	3.2	3.42	100		4.093	4.503	1.862	0.323		11.1

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 (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	3.292	44.852	12453	601	99.37	0.27	0.2694	0.268	0.2807	0.2789	91.369

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]
1.241	0.62		1.241		-4.025

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	14.827
r_dihedral_angle_3_deg	14.298
r_dihedral_angle_1_deg	7.166
r_dihedral_angle_2_deg	6.825
r_lrange_it	5.246
r_mcangle_it	2.276
r_scangle_it	2.192
r_angle_refined_deg	2.022
r_mcbond_it	1.28
r_scbond_it	1.244
r_nbtor_refined	0.304
r_symmetry_nbd_refined	0.241
r_nbd_refined	0.201
r_ncsr_local_group_1	0.178
r_chiral_restr	0.15
r_xyhbond_nbd_refined	0.103
r_symmetry_xyhbond_nbd_refined	0.092
r_gen_planes_refined	0.014
r_bond_refined_d	0.01
r_ext_dist_refined_b	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5097
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms

Software

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