1YZ0 | pdb_00001yz0

R-State AMP Complex Reveals Initial Steps of the Quaternary Transition of Fructose-1,6-bisphosphatase

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.4	298	A54L FBPase (10mg/ml), 25mM Hepes pH7.4, 5 mM MgCl2, 5mM F16P2, 5mM AMP and a precipitant solution [Hepes (100mM, pH 7.4), PEG 3350 (14% w/v), 2-methyl-2,4-pentanediol (21% v/v), and t-butanol (5% v/v)], VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.5	50.1

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 59.74	α = 90
b = 166.14	β = 90
c = 78.94	γ = 90

Symmetry
Space Group	P 21 21 2

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	110	IMAGE PLATE	RIGAKU RAXIS IV	CuKalpha Osmic confocal image system	2001-02-15	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU RU200	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	2	55.38		0.053	6.7		53756	53756			18.9

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)
	2	2.07	96.7		0.272	1.9

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	1EYK	2.07	6	46422	4718	99.7	0.2181	0.218	0.21	0.26	0.25	RANDOM	37.2

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]
10.86			-7.66		-3.2

RMS Deviations
Key	Refinement Restraint Deviation
c_dihedral_angle_d	23.1
c_scangle_it	2.92
c_mcangle_it	2.41
c_scbond_it	2.03
c_mcbond_it	1.46
c_angle_deg	1.2
c_improper_angle_d	0.78
c_bond_d	0.006
c_bond_d_na
c_bond_d_prot
c_angle_d
c_angle_d_na
c_angle_d_prot
c_angle_deg_na
c_angle_deg_prot
c_dihedral_angle_d_na
c_dihedral_angle_d_prot
c_improper_angle_d_na
c_improper_angle_d_prot

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5028
Nucleic Acid Atoms
Solvent Atoms	484
Heterogen Atoms	80

Software

Software
Software Name	Purpose
AMoRE	phasing
CNS	refinement