2GC2

The crystal structure of phosphoglucose isomerase from Pyrococcus furiosus in complex with Fructose 6-phosphate and zinc

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1X8E	PDB ENTRY 1X8E

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	4.6	290	0.1 M ammonium sulphate, 0.1 M sodium acetate trihydrate pH 4.6 and 20% PEG monoethyl ether 2000, 5mM ZnCl2, 50mM fructose 6-phosphate , VAPOR DIFFUSION, HANGING DROP, temperature 290K

Crystal Properties
Matthews coefficient	Solvent content
2.25	45.4

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 70.067	α = 90
b = 73.945	β = 90
c = 74.392	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	IMAGE PLATE	MARRESEARCH		2005-03-21	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU MICROMAX-007

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym 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	52.445	99.9	0.089	0.089	8.1	6.2	23192	23192			26.2

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.1	2.21	99.9	99.9	0.44	0.44	1.7	6.2	3341

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 1X8E	2.1	19.76	23145	23145	1187	99.96	0.176	0.176	0.172	0.246	RANDOM	26.914

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]

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.686
r_dihedral_angle_4_deg	21.214
r_dihedral_angle_3_deg	17.391
r_dihedral_angle_1_deg	7.229
r_scangle_it	4.356
r_scbond_it	2.841
r_mcangle_it	1.816
r_angle_refined_deg	1.761
r_mcbond_it	1.171
r_nbtor_refined	0.31

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.686
r_dihedral_angle_4_deg	21.214
r_dihedral_angle_3_deg	17.391
r_dihedral_angle_1_deg	7.229
r_scangle_it	4.356
r_scbond_it	2.841
r_mcangle_it	1.816
r_angle_refined_deg	1.761
r_mcbond_it	1.171
r_nbtor_refined	0.31
r_symmetry_hbond_refined	0.258
r_symmetry_vdw_refined	0.227
r_nbd_refined	0.202
r_xyhbond_nbd_refined	0.169
r_chiral_restr	0.12
r_bond_refined_d	0.019
r_gen_planes_refined	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3020
Nucleic Acid Atoms
Solvent Atoms	304
Heterogen Atoms	34

Software

Software
Software Name	Purpose
SCALA	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
MOSFLM	data reduction
CCP4	data scaling

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.