1YZ0

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


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1EYK 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.4298A54L 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 coefficientSolvent content
2.550.1

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 59.74α = 90
b = 166.14β = 90
c = 78.94γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray110IMAGE PLATERIGAKU RAXIS IVCuKalpha Osmic confocal image system2001-02-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU RU2001.5418

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
1255.380.0536.7537565375618.9
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
22.0796.70.2721.9

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT1EYK2.07646422471899.70.21810.2180.26RANDOM37.2
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
KeyRefinement Restraint Deviation
c_dihedral_angle_d23.1
c_scangle_it2.92
c_mcangle_it2.41
c_scbond_it2.03
c_mcbond_it1.46
c_angle_deg1.2
c_improper_angle_d0.78
c_bond_d0.006
c_bond_d_na
c_bond_d_prot
RMS Deviations
KeyRefinement Restraint Deviation
c_dihedral_angle_d23.1
c_scangle_it2.92
c_mcangle_it2.41
c_scbond_it2.03
c_mcbond_it1.46
c_angle_deg1.2
c_improper_angle_d0.78
c_bond_d0.006
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 AtomsNumber
Protein Atoms5028
Nucleic Acid Atoms
Solvent Atoms484
Heterogen Atoms80

Software

Software
Software NamePurpose
AMoREphasing
CNSrefinement