5SA3 | pdb_00005sa3

PanDDA analysis group deposition -- Crystal Structure of Trypanosoma brucei Trypanothione reductase in complex with Z2856434874

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8	298	MPD 22%, PEG 3350 14%, imidazole 40 mM pH 8

Crystal Properties
Matthews coefficient	Solvent content
2.29	46.31

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 80.57	α = 90
b = 108.62	β = 90
c = 112.04	γ = 90

Symmetry
Space Group	P 21 21 21

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		2021-01-13		SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04-1	0.91266	Diamond	I04-1

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	1.74	80.57	99.6	0.085	0.092	0.035	0.998	11.3	6.7		100864

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	1.74	1.79	99		2.216	2.392	0.894	0.324		7	7344

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 (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	FOURIER SYNTHESIS	THROUGHOUT	6RB5	1.74	77.99	95896	4900	99.46	0.187	0.1855	0.2	0.2172	0.23	RANDOM	33.662

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]
0.35			-0.68		0.33

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.942
r_dihedral_angle_4_deg	18.26
r_dihedral_angle_3_deg	14.948
r_dihedral_angle_1_deg	6.998
r_mcangle_it	3.208
r_mcbond_it	2.478
r_mcbond_other	2.474
r_angle_refined_deg	1.544
r_angle_other_deg	1.379
r_chiral_restr	0.077

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.942
r_dihedral_angle_4_deg	18.26
r_dihedral_angle_3_deg	14.948
r_dihedral_angle_1_deg	6.998
r_mcangle_it	3.208
r_mcbond_it	2.478
r_mcbond_other	2.474
r_angle_refined_deg	1.544
r_angle_other_deg	1.379
r_chiral_restr	0.077
r_bond_refined_d	0.009
r_gen_planes_refined	0.008
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	7360
Nucleic Acid Atoms
Solvent Atoms	534
Heterogen Atoms	170

Software

Software
Software Name	Purpose
REFMAC	refinement
Aimless	data scaling
PDB_EXTRACT	data extraction
XDS	data reduction
REFMAC	phasing

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.