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The crystal structure of phosphoglucose isomerase from Pyrococcus furiosus in complex with mannose 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, 5mM ZnCl2, 5mM mannose 6-phosphate, VAPOR DIFFUSION, HANGING DROP, temperature 290K
Crystal Properties Matthews coefficient Solvent content 2.28 45.99
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 70.346 α = 90 b = 74.016 β = 90 c = 74.835 γ = 90
Symmetry Space Group P 21 21 21
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 2005-03-29 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 2.1 74.835 100 0.104 0.104 5.9 6.9 23477 23477 22.9
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) 2.1 2.21 100 100 0.366 0.366 2 6.6 3361
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 (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 2.1 19.85 23440 1202 99.99 0.162 0.162 0.158 0.158 0.235 0.2325 RANDOM 25.049
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
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.343 r_dihedral_angle_3_deg 15.8 r_dihedral_angle_4_deg 14.372 r_scangle_it 12.173 r_scbond_it 9.139 r_mcangle_it 7.819 r_mcbond_it 6.85 r_dihedral_angle_1_deg 6.472 r_angle_refined_deg 1.246 r_nbtor_refined 0.306
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.343 r_dihedral_angle_3_deg 15.8 r_dihedral_angle_4_deg 14.372 r_scangle_it 12.173 r_scbond_it 9.139 r_mcangle_it 7.819 r_mcbond_it 6.85 r_dihedral_angle_1_deg 6.472 r_angle_refined_deg 1.246 r_nbtor_refined 0.306 r_symmetry_hbond_refined 0.232 r_symmetry_vdw_refined 0.199 r_nbd_refined 0.181 r_xyhbond_nbd_refined 0.116 r_chiral_restr 0.081 r_metal_ion_refined 0.061 r_bond_refined_d 0.009 r_gen_planes_refined 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3020 Nucleic Acid Atoms Solvent Atoms 353 Heterogen Atoms 34
Software Software Software Name Purpose SCALA data scaling MOLREP phasing REFMAC refinement PDB_EXTRACT data extraction MOSFLM data reduction CCP4 data scaling