2ZJ4

Isomerase domain of human glucose:fructose-6-phosphate amidotransferase


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2ZJ3PDB ENTRY 2ZJ3

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP8.527712% Isoporpanol, 0.04M Tris, 0.08M Ammonium acetate, 12% glycerol 10-fold excess of 2-deoxy-2-aminoglucitol-6-phosphate, pH 8.50, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
2.5551.79

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 78.927α = 90
b = 78.927β = 90
c = 277.323γ = 90
Symmetry
Space GroupI 41 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS V2003-08-04MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSPRING-8 BEAMLINE BL32B2SPring-8BL32B2

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
12.239.5398.422501

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 REPLACEMENTTHROUGHOUTPDB ENTRY 2ZJ32.23821357114498.390.160.1580.208RANDOM20.568
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]
0.010.01-0.02
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.79
r_dihedral_angle_4_deg20.724
r_dihedral_angle_3_deg15.697
r_dihedral_angle_1_deg6.404
r_scangle_it4.334
r_scbond_it3.106
r_angle_refined_deg1.778
r_mcangle_it1.612
r_angle_other_deg1.454
r_mcbond_it1.437
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.79
r_dihedral_angle_4_deg20.724
r_dihedral_angle_3_deg15.697
r_dihedral_angle_1_deg6.404
r_scangle_it4.334
r_scbond_it3.106
r_angle_refined_deg1.778
r_mcangle_it1.612
r_angle_other_deg1.454
r_mcbond_it1.437
r_symmetry_vdw_other0.289
r_symmetry_hbond_refined0.24
r_mcbond_other0.238
r_nbd_refined0.23
r_nbd_other0.196
r_symmetry_vdw_refined0.187
r_xyhbond_nbd_refined0.185
r_nbtor_refined0.171
r_chiral_restr0.121
r_nbtor_other0.088
r_bond_refined_d0.021
r_gen_planes_refined0.007
r_bond_other_d0.001
r_gen_planes_other0.001
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2863
Nucleic Acid Atoms
Solvent Atoms267
Heterogen Atoms16

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing