2GC3 | pdb_00002gc3

The crystal structure of phosphoglucose isomerase from Pyrococcus furiosus in complex with mannose 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	0.05 M ammonium sulphate, 0.1 M sodium acetate pH 4.6, 20% PEG monoethyl ether 2000, 5mM ZnCl2, 5mM mannose 6-phosphate, VAPOR DIFFUSION, HANGING DROP, temperature 290K

Crystal Properties
Matthews coefficient	Solvent content
2.28	45.99

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 70.346	α = 90
b = 74.016	β = 90
c = 74.835	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	Osmic Varimax	2005-03-29	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	74.835	100	0.104	0.104	5.9	6.9	23477	23477			22.9

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)
	2.1	2.21	100	100	0.366	0.366	2	6.6	3361

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 (All)	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 1X8E	2.1	19.85	23440	1202	99.99	0.162	0.162	0.158	0.16	0.235	0.23	RANDOM	25.049

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]
0.01			-0.01

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.343
r_dihedral_angle_3_deg	15.8
r_dihedral_angle_4_deg	14.372
r_scangle_it	12.173
r_scbond_it	9.139
r_mcangle_it	7.819
r_mcbond_it	6.85
r_dihedral_angle_1_deg	6.472
r_angle_refined_deg	1.246
r_nbtor_refined	0.306

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.343
r_dihedral_angle_3_deg	15.8
r_dihedral_angle_4_deg	14.372
r_scangle_it	12.173
r_scbond_it	9.139
r_mcangle_it	7.819
r_mcbond_it	6.85
r_dihedral_angle_1_deg	6.472
r_angle_refined_deg	1.246
r_nbtor_refined	0.306
r_symmetry_hbond_refined	0.232
r_symmetry_vdw_refined	0.199
r_nbd_refined	0.181
r_xyhbond_nbd_refined	0.116
r_chiral_restr	0.081
r_metal_ion_refined	0.061
r_bond_refined_d	0.009
r_gen_planes_refined	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3020
Nucleic Acid Atoms
Solvent Atoms	353
Heterogen Atoms	34

Software

Software
Software Name	Purpose
SCALA	data scaling
MOLREP	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.