2Q8M | pdb_00002q8m

T-like Fructose-1,6-bisphosphatase from Escherichia coli with AMP, Glucose 6-phosphate, and Fructose 1,6-bisphosphate bound

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2GQ1	PDB ENTRY 2GQ1

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7	295	Protein solution: (15 mg/mL enzyme (pH 7.4), 20 mM dithiothreitol (DTT), 0.1 mM EDTA, 5 mM Fru-1,6-P2, 5 mM MgCl2, and 5 mM AMP) Precipitant solution: (50 mM MES-NaOH, pH 6.5, 13% (w/v) PEG 10,000, and 20% (w/v) sucrose), pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 295.0K

Crystal Properties
Matthews coefficient	Solvent content
3.45	64.4

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 124.64	α = 90
b = 124.64	β = 90
c = 132.28	γ = 90

Symmetry
Space Group	P 41 2 2

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	NOIR-1		2005-01-29	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 4.2.2	0.979	ALS	4.2.2

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	2.05	39.41	96.6	0.068	0.068	9.2	2.43	63542	63542

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	2.05	2.12	95.7		0.255	0.255	3.5	2.47	6202

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 2GQ1	2.05	37.77	63536	63536	6416	96.5	0.212	0.212	0.209	0.21	0.235	RANDOM	31.8

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]
-1.71			-1.71		3.43

RMS Deviations
Key	Refinement Restraint Deviation
c_dihedral_angle_d	22.8
c_scangle_it	3.24
c_scbond_it	2.36
c_mcangle_it	2.2
c_mcbond_it	1.38
c_angle_deg	1.2
c_improper_angle_d	0.74
c_bond_d	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4868
Nucleic Acid Atoms
Solvent Atoms	312
Heterogen Atoms	109

Software

Software
Software Name	Purpose
d*TREK	data processing
CNS	refinement
PDB_EXTRACT	data extraction
CrystalClear	data collection
d*TREK	data reduction
d*TREK	data scaling
AMoRE	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.