7E3G

Crystal structure of Trypanosoma brucei cathepsin B R91C/T223C mutant in the living cell

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	IN CELL		298

Crystal Properties
Matthews coefficient	Solvent content
2.74	55.1

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 124.08	α = 90
b = 124.08	β = 90
c = 52.96	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		2018-07-17	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	3.86	50	96.3	0.918	3.48	5.4		4069

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	3.86	4.09			0.558

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	3.86	48.756	4067	203	96.764	0.178	0.1766	0.2138	74.122

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]
-1.029			-1.029		2.058

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.464
r_dihedral_angle_3_deg	19.772
r_dihedral_angle_4_deg	19.397
r_lrange_it	11.578
r_lrange_other	11.576
r_dihedral_angle_1_deg	8.8
r_scangle_it	8.066
r_scangle_other	8.065
r_mcangle_it	8.027
r_mcangle_other	8.027
r_mcbond_it	4.943
r_mcbond_other	4.932
r_scbond_it	4.878
r_scbond_other	4.872
r_angle_refined_deg	1.635
r_angle_other_deg	1.204
r_nbd_refined	0.232
r_symmetry_nbd_other	0.207
r_nbtor_refined	0.181
r_xyhbond_nbd_refined	0.181
r_nbd_other	0.17
r_symmetry_xyhbond_nbd_refined	0.152
r_symmetry_nbd_refined	0.143
r_symmetry_nbtor_other	0.08
r_chiral_restr	0.056
r_bond_refined_d	0.006
r_gen_planes_refined	0.006
r_gen_planes_other	0.002
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2377
Nucleic Acid Atoms
Solvent Atoms	3
Heterogen Atoms	67

Software

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