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The crystal structure of phosphoglucose isomerase from Pyrococcus furiosus in complex with Fructose 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 0.1 M ammonium sulphate, 0.1 M sodium acetate trihydrate pH 4.6 and 20% PEG monoethyl ether 2000, 5mM ZnCl2, 50mM fructose 6-phosphate , VAPOR DIFFUSION, HANGING DROP, temperature 290K
Crystal Properties Matthews coefficient Solvent content 2.25 45.4
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 70.067 α = 90 b = 73.945 β = 90 c = 74.392 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 2005-03-21 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 52.445 99.9 0.089 0.089 8.1 6.2 23192 23192 26.2
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 2.1 2.21 99.9 99.9 0.44 0.44 1.7 6.2 3341
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 2.1 19.76 23145 23145 1187 99.96 0.176 0.176 0.172 0.1714 0.246 0.2395 RANDOM 26.914
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.686 r_dihedral_angle_4_deg 21.214 r_dihedral_angle_3_deg 17.391 r_dihedral_angle_1_deg 7.229 r_scangle_it 4.356 r_scbond_it 2.841 r_mcangle_it 1.816 r_angle_refined_deg 1.761 r_mcbond_it 1.171 r_nbtor_refined 0.31
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.686 r_dihedral_angle_4_deg 21.214 r_dihedral_angle_3_deg 17.391 r_dihedral_angle_1_deg 7.229 r_scangle_it 4.356 r_scbond_it 2.841 r_mcangle_it 1.816 r_angle_refined_deg 1.761 r_mcbond_it 1.171 r_nbtor_refined 0.31 r_symmetry_hbond_refined 0.258 r_symmetry_vdw_refined 0.227 r_nbd_refined 0.202 r_xyhbond_nbd_refined 0.169 r_chiral_restr 0.12 r_bond_refined_d 0.019 r_gen_planes_refined 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3020 Nucleic Acid Atoms Solvent Atoms 304 Heterogen Atoms 34
Software Software Software Name Purpose SCALA data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction MOSFLM data reduction CCP4 data scaling