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The crystal structure of the P132A, 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 0.35 M MgCl2, 0.1 M sodium acetate PH 5.5 and 19% PEG4000, VAPOR DIFFUSION, HANGING DROP, temperature 290K
Crystal Properties Matthews coefficient Solvent content 2.18 43.64
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 87.85 α = 90 b = 43.28 β = 122.9 c = 58.45 γ = 90
Symmetry Space Group C 1 2 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 PIXEL DECTRIS PILATUS 6M Diamond IO3 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 1.41 28.92 91.2 0.036 13 3.1 32797 32797
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 1.41 1.44 55.4 0.349 2.1 2.4 1460
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 (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 1.41 28.92 32797 31134 1663 100 0.15336 0.15009 0.1555 0.21388 0.2147 RANDOM 26.299
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] -1.79 -1.83 2.35 -2.56
RMS Deviations Key Refinement Restraint Deviation r_scbond_it 86.29 r_scangle_it 78.163 r_rigid_bond_restr 52.302 r_mcbond_it 37.221 r_mcangle_it 35.504 r_dihedral_angle_2_deg 29.068 r_mcbond_other 21.17 r_dihedral_angle_4_deg 12.722 r_dihedral_angle_3_deg 10.587 r_dihedral_angle_1_deg 5.954
RMS Deviations Key Refinement Restraint Deviation r_scbond_it 86.29 r_scangle_it 78.163 r_rigid_bond_restr 52.302 r_mcbond_it 37.221 r_mcangle_it 35.504 r_dihedral_angle_2_deg 29.068 r_mcbond_other 21.17 r_dihedral_angle_4_deg 12.722 r_dihedral_angle_3_deg 10.587 r_dihedral_angle_1_deg 5.954 r_angle_refined_deg 1.064 r_angle_other_deg 0.726 r_chiral_restr 0.063 r_bond_refined_d 0.006 r_gen_planes_refined 0.004 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1510 Nucleic Acid Atoms Solvent Atoms 195 Heterogen Atoms 32
Software Software Software Name Purpose GDA data collection PHASER phasing REFMAC refinement xia2 data reduction xia2 data scaling