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Isomerase domain of human glucose:fructose-6-phosphate amidotransferase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2ZJ3 PDB ENTRY 2ZJ3
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 277 12% 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 coefficient Solvent content 2.55 51.79
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 78.927 α = 90 b = 78.927 β = 90 c = 277.323 γ = 90
Symmetry Space Group I 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 IMAGE PLATE RIGAKU RAXIS V 2003-08-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL32B2 SPring-8 BL32B2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.2 39.53 98.4 22501
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 2ZJ3 2.2 38 21357 1144 98.39 0.16 0.158 0.208 0.1651 RANDOM 20.568
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] 0.01 0.01 -0.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.79 r_dihedral_angle_4_deg 20.724 r_dihedral_angle_3_deg 15.697 r_dihedral_angle_1_deg 6.404 r_scangle_it 4.334 r_scbond_it 3.106 r_angle_refined_deg 1.778 r_mcangle_it 1.612 r_angle_other_deg 1.454 r_mcbond_it 1.437
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.79 r_dihedral_angle_4_deg 20.724 r_dihedral_angle_3_deg 15.697 r_dihedral_angle_1_deg 6.404 r_scangle_it 4.334 r_scbond_it 3.106 r_angle_refined_deg 1.778 r_mcangle_it 1.612 r_angle_other_deg 1.454 r_mcbond_it 1.437 r_symmetry_vdw_other 0.289 r_symmetry_hbond_refined 0.24 r_mcbond_other 0.238 r_nbd_refined 0.23 r_nbd_other 0.196 r_symmetry_vdw_refined 0.187 r_xyhbond_nbd_refined 0.185 r_nbtor_refined 0.171 r_chiral_restr 0.121 r_nbtor_other 0.088 r_bond_refined_d 0.021 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001 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 Atoms Number Protein Atoms 2863 Nucleic Acid Atoms Solvent Atoms 267 Heterogen Atoms 16
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing