4H46

Crystal Structure of AMP complexes of NEM modified Porcine Liver Fructose-1,6-bisphosphatase


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2F3DPDB ENTRY 2F3D

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.5298PEG3350, t-butyl alcohol, 1,2-ethanediol, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.7755.52

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 62.561α = 90
b = 78.673β = 90
c = 164.928γ = 90
Symmetry
Space GroupI 2 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS2011-11-24MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU1.5418

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
12.542.195.60.1117.23.73145011386322
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)
12.52.5998.40.3442.63.62

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 2F3D2.541.3144931314769495.50.197450.194490.25644RANDOM25.162
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]
-0.010.02-0.01
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.527
r_dihedral_angle_4_deg25.738
r_dihedral_angle_3_deg18.438
r_dihedral_angle_1_deg6.359
r_scangle_it4.007
r_scbond_it2.636
r_angle_refined_deg2.052
r_mcangle_it1.956
r_mcbond_it1.053
r_chiral_restr0.136
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.527
r_dihedral_angle_4_deg25.738
r_dihedral_angle_3_deg18.438
r_dihedral_angle_1_deg6.359
r_scangle_it4.007
r_scbond_it2.636
r_angle_refined_deg2.052
r_mcangle_it1.956
r_mcbond_it1.053
r_chiral_restr0.136
r_bond_refined_d0.022
r_gen_planes_refined0.01
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2439
Nucleic Acid Atoms
Solvent Atoms101
Heterogen Atoms54

Software

Software
Software NamePurpose
d*TREKdata scaling
d*TREKdata reduction
MOLREPphasing
REFMACrefinement
PDB_EXTRACTdata extraction
CrystalCleardata collection