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The crystal structure of the P132R, Y133G mutant of Pyrococcus furiosus phosphoglucose isomerase in complex with manganese and 5-phospho-D-arabinonate.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1X7N PDB ENTRY 1X7N
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.5 290 0.35M magnesium chloride, 0.1M sodium acetate, 19% PEG4000, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 290K
Crystal Properties Matthews coefficient Solvent content 2.4 48.79
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 72.95 α = 90 b = 74.47 β = 90 c = 75.9 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 PIXEL DECTRIS PILATUS 6M Diamond I03 2011-05-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.97630 Diamond I03
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 2.04 26.58 99.6 0.074 7 6.3 26994 26994
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.04 2.09 99.9 0.219 6.4 1969
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 1X7N 2.04 26.58 26994 25635 1356 100 0.22 0.22125 0.21723 0.2174 0.29492 0.2944 RANDOM 42.791
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] -0.69 -2.43 3.13
RMS Deviations Key Refinement Restraint Deviation r_scbond_it 98.411 r_scangle_it 73.77 r_mcbond_it 46.146 r_mcangle_it 44.184 r_dihedral_angle_2_deg 32.896 r_dihedral_angle_4_deg 17.472 r_dihedral_angle_3_deg 15.413 r_dihedral_angle_1_deg 6.479 r_angle_refined_deg 1.417 r_chiral_restr 0.099
RMS Deviations Key Refinement Restraint Deviation r_scbond_it 98.411 r_scangle_it 73.77 r_mcbond_it 46.146 r_mcangle_it 44.184 r_dihedral_angle_2_deg 32.896 r_dihedral_angle_4_deg 17.472 r_dihedral_angle_3_deg 15.413 r_dihedral_angle_1_deg 6.479 r_angle_refined_deg 1.417 r_chiral_restr 0.099 r_bond_refined_d 0.013 r_gen_planes_refined 0.006 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3032 Nucleic Acid Atoms Solvent Atoms 140 Heterogen Atoms 48
Software Software Software Name Purpose GDA data collection PHASER phasing REFMAC refinement xia2 data reduction xia2 data scaling