7S2H | pdb_00007s2h

Crystal structure of Trypanosoma cruzi glucokinase in the apo form (open conformation)

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	7.5	295	1.0 uL of 7.4 mg/mL wt-TcGlcK in buffered solution [50 mM HEPES (pH 7.5), 0.2 M imidazole, 2 mM magnesium chloride] + 1.0 uL of precipitant solution [14% (w/v) PEG 3350, 0.1 M sodium citrate tribasic] was equilibrated against 85 uL of the precipitant solution using a 96-well sitting-drop plate (Innovadyne)

Crystal Properties
Matthews coefficient	Solvent content
2.37	48.1

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 67.304	α = 90
b = 78.92	β = 101.3
c = 76.847	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	RAYONIX MX300-HS		2014-06-27	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 22-ID	1.0000	APS	22-ID

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	1.8	40	100	0.083	0.031	41.9	7.5		72625		-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	1.8	1.83			0.949	0.344	0.833	2.8

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	MOLECULAR REPLACEMENT	THROUGHOUT	2Q2R	1.8	35.92	68906	3676	99.27	0.1664	0.1649	0.17	0.1937	0.2	RANDOM	33.742

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]
-3.21			0.93		2.11

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.636
r_dihedral_angle_4_deg	15.309
r_dihedral_angle_3_deg	12.638
r_dihedral_angle_1_deg	6.316
r_angle_other_deg	2.347
r_angle_refined_deg	1.719
r_chiral_restr	0.087
r_bond_other_d	0.036
r_gen_planes_other	0.019
r_bond_refined_d	0.013

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.636
r_dihedral_angle_4_deg	15.309
r_dihedral_angle_3_deg	12.638
r_dihedral_angle_1_deg	6.316
r_angle_other_deg	2.347
r_angle_refined_deg	1.719
r_chiral_restr	0.087
r_bond_other_d	0.036
r_gen_planes_other	0.019
r_bond_refined_d	0.013
r_gen_planes_refined	0.012

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5642
Nucleic Acid Atoms
Solvent Atoms	548
Heterogen Atoms	24

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.