3UJH | pdb_00003ujh

Crystal structure of substrate-bound Glucose-6-phosphate isomerase from Toxoplasma gondii

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3PR3	pdb entry 3PR3

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8.5	290	Internal tracking number 226935D6. The crystallant was JCSG screen condition D6: 30% PEG 8000, 0.1 M Tris 8.5, 200 mM MgCl2. The protein solution was TogoA.17127.a.A1 PW28176 at 26.2 mg/mL in a stabilizing buffer of 500 mM NaCl, 25 mM HEPES, 5% glycerol, 0.025% azide, 2 mM DTT, pH 7.0 with 10mM Glucose-6-phosphate. 0.4 + 0.4 uL sitting drop vapor diffusion. Cryoprotection: 20% ethylene glycol., vapor diffusion, sitting drop, temperature 290K, VAPOR DIFFUSION, SITTING DROP

Crystal Properties
Matthews coefficient	Solvent content
2.36	47.8

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 77.82	α = 90
b = 111.36	β = 90
c = 137.28	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	CCD	RIGAKU SATURN 944+		2011-10-28	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU FR-E SUPERBRIGHT	1.541780

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	2.1	50	96.1	0.156	8.86	4.1		67619		-3	22.775

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.1	2.15	78.5		0.529	2.9	3.7

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	pdb entry 3PR3	2.1	50	67567	3415	96.15	0.173	0.171	0.18	0.219	0.22	RANDOM	16.471

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]
0.95			-0.31		-0.64

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.09
r_dihedral_angle_4_deg	15.144
r_dihedral_angle_3_deg	13.82
r_dihedral_angle_1_deg	5.87
r_angle_refined_deg	1.519
r_angle_other_deg	0.951
r_chiral_restr	0.087
r_bond_refined_d	0.012
r_gen_planes_refined	0.007
r_bond_other_d	0.001

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.09
r_dihedral_angle_4_deg	15.144
r_dihedral_angle_3_deg	13.82
r_dihedral_angle_1_deg	5.87
r_angle_refined_deg	1.519
r_angle_other_deg	0.951
r_chiral_restr	0.087
r_bond_refined_d	0.012
r_gen_planes_refined	0.007
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	8840
Nucleic Acid Atoms
Solvent Atoms	742
Heterogen Atoms	41

Software

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

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.