5OML

Crystal structure of Trypanosoma Brucei PEX14 N-terminal domain in complex with small molecules to investigate the water envelope

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		277	0.22M Li2SO4 0.1M Tris-HCl pH8.5 29% PEG 4000

Crystal Properties
Matthews coefficient	Solvent content
2.57	52.12

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 35.863	α = 90
b = 116.368	β = 101.46
c = 38.962	γ = 90

Symmetry
Space Group	P 1 21 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-F		2017-04-14	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PETRA III, DESY BEAMLINE P11	1.033	PETRA III, DESY	P11

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	1.5	20	95.6	0.053	0.067	0.996	9.04	2.501		48921		-3	29.403

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	1.5	1.54	88.9		0.728	0.926	0.548	1.33	2.48

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	5AON	1.5	20	46462	2440	97.88	0.1776	0.1762	0.2021	RANDOM	24.751

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]
-0.3		-0.78	1.35		-0.68

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.465
r_dihedral_angle_4_deg	21.351
r_dihedral_angle_3_deg	14.664
r_dihedral_angle_1_deg	4.634
r_angle_other_deg	2.533
r_angle_refined_deg	2.424
r_chiral_restr	0.126
r_bond_refined_d	0.027
r_bond_other_d	0.017
r_gen_planes_refined	0.014

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.465
r_dihedral_angle_4_deg	21.351
r_dihedral_angle_3_deg	14.664
r_dihedral_angle_1_deg	4.634
r_angle_other_deg	2.533
r_angle_refined_deg	2.424
r_chiral_restr	0.126
r_bond_refined_d	0.027
r_bond_other_d	0.017
r_gen_planes_refined	0.014
r_gen_planes_other	0.01

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2076
Nucleic Acid Atoms
Solvent Atoms	392
Heterogen Atoms	197

Software

Software
Software Name	Purpose
XSCALE	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
PHASER	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 R01GM133198.