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The crystal structure of phosphoglucose isomerase from Pyrococcus furiosus in complex with sorbitol 6-phosphate and zinc
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1X8E PDB ENTRY 1X8E
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.6 290 0.05 M ammonium sulphate, 0.1 M sodium acetate pH 4.6, 20% PEG monoethyl ether 2000, 5 mM D-sorbitol 6-phosphate, 5mM ZnCl2, VAPOR DIFFUSION, HANGING DROP, temperature 290K
Crystal Properties Matthews coefficient Solvent content 2.51 50.98
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 42.311 α = 90 b = 72.857 β = 103.57 c = 71.64 γ = 90
Symmetry Space Group P 1 21 1
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 MARRESEARCH Osmic Varimax 2005-03-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 1.95 69.673 92.1 0.062 0.062 9.6 4.6 28380 28380 25.9
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1.95 2.06 88.2 88.5 0.379 0.379 2 4.5
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 PDB ENTRY 1X8E 1.95 19.92 28346 28346 1436 91.75 0.201 0.201 0.198 0.1931 0.255 0.2472 RANDOM 25.979
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 0.09 0.01 0.03
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.661 r_dihedral_angle_4_deg 15.698 r_dihedral_angle_3_deg 15.424 r_dihedral_angle_1_deg 6.342 r_scangle_it 2.23 r_angle_refined_deg 1.653 r_scbond_it 1.455 r_mcangle_it 1.102 r_mcbond_it 0.65 r_nbtor_refined 0.309
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.661 r_dihedral_angle_4_deg 15.698 r_dihedral_angle_3_deg 15.424 r_dihedral_angle_1_deg 6.342 r_scangle_it 2.23 r_angle_refined_deg 1.653 r_scbond_it 1.455 r_mcangle_it 1.102 r_mcbond_it 0.65 r_nbtor_refined 0.309 r_symmetry_vdw_refined 0.203 r_nbd_refined 0.187 r_xyhbond_nbd_refined 0.127 r_symmetry_hbond_refined 0.126 r_metal_ion_refined 0.117 r_symmetry_metal_ion_refined 0.106 r_chiral_restr 0.085 r_bond_refined_d 0.01 r_gen_planes_refined 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3027 Nucleic Acid Atoms Solvent Atoms 307 Heterogen Atoms 35
Software Software Software Name Purpose SCALA data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction MOSFLM data reduction CCP4 data scaling