7E3F

Crystal structure of Trypanosoma brucei cathepsin B Y217C/S275C mutant

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	IN CELL		293	In cell crystallization

Crystal Properties
Matthews coefficient	Solvent content
2.79	55.87

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 123.65	α = 90
b = 123.65	β = 90
c = 54.28	γ = 90

Symmetry
Space Group	P 42 21 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 PILATUS3 6M		2019-12-05	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SPRING-8 BEAMLINE BL32XU	1.0	SPring-8	BL32XU

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	2.35	50	100	0.979	6.9	243		18117

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	2.35	2.37			0.416

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Work	R-Free	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	4hwy	2.35	49.751	18080	922	99.978	0.221	0.2189	0.2572	30.125

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]
1.22			1.22		-2.439

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.56
r_dihedral_angle_4_deg	17.574
r_dihedral_angle_3_deg	17.221
r_dihedral_angle_1_deg	7.308
r_lrange_other	5.89
r_lrange_it	5.889
r_scangle_it	4.724
r_scangle_other	4.723
r_mcangle_it	3.454
r_mcangle_other	3.454
r_scbond_it	3.012
r_scbond_other	3.012
r_mcbond_it	2.188
r_mcbond_other	2.187
r_angle_refined_deg	1.683
r_angle_other_deg	1.237
r_symmetry_nbd_refined	0.287
r_nbd_other	0.19
r_nbd_refined	0.18
r_symmetry_xyhbond_nbd_refined	0.171
r_symmetry_nbd_other	0.169
r_nbtor_refined	0.166
r_xyhbond_nbd_refined	0.146
r_symmetry_nbtor_other	0.081
r_chiral_restr	0.075
r_bond_refined_d	0.009
r_gen_planes_refined	0.006
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2379
Nucleic Acid Atoms
Solvent Atoms	36
Heterogen Atoms	67

Software

Software
Software Name	Purpose
REFMAC	refinement
XSCALE	data scaling
PHENIX	phasing
XDS	data processing