6SPT | pdb_00006spt

High resolution crystal structure of N-terminal domain of PEX14 from Trypanosoma brucei in complex with the fist compound with sub-micromolar trypanocidal activity

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		298	0.2M MgCl2, 0.1 M Tris pH 8, 20% (w/v) PEG 6000

Crystal Properties
Matthews coefficient	Solvent content
2.46	50.05

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 45.935	α = 90
b = 45.935	β = 90
c = 63.733	γ = 120

Symmetry
Space Group	P 32 2 1

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		2017-02-06	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID29	0.97625	ESRF	ID29

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim 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	1.2	39.78	93.7	0.072	0.082	0.996	9.42	3.93		23334			15.045

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.2	1.3	86.3		0.291	0.345	0.89	2.97	3.367

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 (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	1.2	39.78	22179	1155	93.7	0.1106	0.1084	0.11	0.1524	0.15	RANDOM	13.924

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]
-0.03	-0.01		-0.03		0.09

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.458
r_sphericity_free	28.747
r_dihedral_angle_3_deg	15.104
r_sphericity_bonded	12.171
r_dihedral_angle_4_deg	10.064
r_rigid_bond_restr	6.465
r_dihedral_angle_1_deg	4.628
r_angle_refined_deg	2.67
r_angle_other_deg	1.289
r_chiral_restr	0.134

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.458
r_sphericity_free	28.747
r_dihedral_angle_3_deg	15.104
r_sphericity_bonded	12.171
r_dihedral_angle_4_deg	10.064
r_rigid_bond_restr	6.465
r_dihedral_angle_1_deg	4.628
r_angle_refined_deg	2.67
r_angle_other_deg	1.289
r_chiral_restr	0.134
r_bond_refined_d	0.028
r_gen_planes_refined	0.012
r_gen_planes_other	0.004
r_bond_other_d	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	552
Nucleic Acid Atoms
Solvent Atoms	136
Heterogen Atoms	68

Software

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

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.