1QXR | pdb_00001qxr

Crystal structure of phosphoglucose isomerase from Pyrococcus furiosus in complex with 5-phosphoarabinonate

X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5.6	295	25% PEG 4000, 0.2M ammonium acetate, 0.1M sodium acetate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 295K

Crystal Properties
Matthews coefficient	Solvent content
2.3	45

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 36	α = 73.7
b = 39.7	β = 78.5
c = 74.7	γ = 72.6

Symmetry
Space Group	P 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	IMAGE PLATE	RIGAKU RAXIS IV	mirrors	2003-07-04	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU RUH3R	1.5418

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	1.7	36.8	92.5	0.041	12.5	2.7		38279			23.6

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)
	1.7	1.76	88.2		0.297	3.3	2.7	3618

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	REFINEMENT	THROUGHOUT	1QXJ	1.7	15	38161	1940	92.3	0.223	0.223	0.221	0.22	0.264	0.26	RANDOM	29.621

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]
1.16	-0.72	-0.46	-0.23	1.61	-1.22

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	19.894
r_dihedral_angle_1_deg	4.728
r_scangle_it	3.617
r_scbond_it	2.27
r_angle_refined_deg	1.54
r_mcangle_it	1.487
r_mcbond_it	0.84
r_nbd_refined	0.218
r_symmetry_hbond_refined	0.158
r_symmetry_vdw_refined	0.156

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	19.894
r_dihedral_angle_1_deg	4.728
r_scangle_it	3.617
r_scbond_it	2.27
r_angle_refined_deg	1.54
r_mcangle_it	1.487
r_mcbond_it	0.84
r_nbd_refined	0.218
r_symmetry_hbond_refined	0.158
r_symmetry_vdw_refined	0.156
r_xyhbond_nbd_refined	0.142
r_chiral_restr	0.107
r_bond_refined_d	0.013
r_gen_planes_refined	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3004
Nucleic Acid Atoms
Solvent Atoms	126
Heterogen Atoms	32

Software

Software
Software Name	Purpose
REFMAC	refinement
CrystalClear	data reduction
CrystalClear	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.