7S2P

Crystal structure of the F337L mutation of Trypanosoma cruzi glucokinase in complex with inhibitor CBZ-GlcN

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2Q2R

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		295	A ligand-free TcGlcK(F337L) crystal was soaked in 1.0 mM CBZ-GlcN, 5.0% (v/v) DMSO, 0.1 M sodium citrate (pH 7.0), 15% (w/v) PEG 3,350 for 24 hours

Crystal Properties
Matthews coefficient	Solvent content
2.45	49.79

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 68.227	α = 90
b = 78.951	β = 94.86
c = 77.027	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	CCD	ADSC QUANTUM 315r		2014-06-27	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 14-ID-B	0.9792	APS	14-ID-B

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	Rrim I (All)	Rpim I (All)	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	2.35	40	99.1	0.052	0.027	35.3	3.7		33656		-3

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.35	2.39	98.2		0.718	0.372	0.702	2	3.6

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	2Q2R	2.35	38.4	31970	1679	98.69	0.2041	0.2015	0.255	RANDOM	71.278

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]
-2.67		1.31	2.15		0.29

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.739
r_dihedral_angle_4_deg	18.318
r_dihedral_angle_3_deg	13.979
r_dihedral_angle_1_deg	7.257
r_angle_other_deg	2.353
r_angle_refined_deg	1.67
r_chiral_restr	0.077
r_bond_other_d	0.035
r_gen_planes_other	0.013
r_bond_refined_d	0.012

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.739
r_dihedral_angle_4_deg	18.318
r_dihedral_angle_3_deg	13.979
r_dihedral_angle_1_deg	7.257
r_angle_other_deg	2.353
r_angle_refined_deg	1.67
r_chiral_restr	0.077
r_bond_other_d	0.035
r_gen_planes_other	0.013
r_bond_refined_d	0.012
r_gen_planes_refined	0.009

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5627
Nucleic Acid Atoms
Solvent Atoms	52
Heterogen Atoms	49

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-3000	data reduction
HKL-3000	data scaling
MOLREP	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.