7NVP | pdb_00007nvp

Trypanothione reductase from Trypanosoma brucei in complex with N-{4-methoxy-3-[(4-methoxyphenyl)sulfamoyl]phenyl}-5-nitrothiophene-2-carboxamide

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2WBA

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293.15	TbTR (10 mg/ml) in 20 mM HEPES pH 7.4; cocrystallisation with 2 mM A1/7 (incubation O/N, 283.15 K). Hanging drop vapor diffusion method + seeding, Crystallisation conditions: 100 mM Hepes pH 7-8 + 2.2-2.3 M Ammonium sulphate

Crystal Properties
Matthews coefficient	Solvent content
3.28	62.51

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 66.096	α = 90
b = 133.334	β = 90
c = 158.912	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		2019-09-26	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ELETTRA BEAMLINE 11.2C	1.030000	ELETTRA	11.2C

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	2.153	158.912	99.7	0.1439	0.1499	0.04142	0.998	12.14	12.9		76940			41.4

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.153	2.23	98.92		1.595	0.4854	0.635	1.64	11.5

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	2WBA	2.153	102.143	76635	3832	99.71	0.242	0.2399	0.24	0.2777	0.28	51.112

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]
-0.472			0.552		-0.08

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.977
r_dihedral_angle_3_deg	14.816
r_dihedral_angle_4_deg	14.707
r_lrange_it	10.334
r_lrange_other	10.319
r_dihedral_angle_1_deg	7.203
r_scangle_it	7.014
r_scangle_other	6.991
r_mcangle_it	6.607
r_mcangle_other	6.607
r_scbond_it	4.696
r_scbond_other	4.666
r_mcbond_it	4.618
r_mcbond_other	4.617
r_angle_refined_deg	1.522
r_angle_other_deg	1.227
r_symmetry_xyhbond_nbd_refined	0.36
r_nbd_other	0.338
r_xyhbond_nbd_refined	0.24
r_nbd_refined	0.213
r_symmetry_nbd_other	0.19
r_nbtor_refined	0.163
r_symmetry_nbd_refined	0.153
r_symmetry_xyhbond_nbd_other	0.109
r_symmetry_nbtor_other	0.074
r_chiral_restr	0.065
r_bond_refined_d	0.008
r_gen_planes_refined	0.008
r_gen_planes_other	0.003
r_bond_other_d	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	7438
Nucleic Acid Atoms
Solvent Atoms	175
Heterogen Atoms	209

Software

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