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Crystal structure of native phosphoglucose/phosphomannose isomerase from Pyrobaculum aerophilum
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 295 25% polyethylene glycol 8000, 0.22M ammonium sulphate, 100mM Tris, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal Properties Matthews coefficient Solvent content 2.1 42
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 55.1 α = 90 b = 100.8 β = 113.2 c = 55.8 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 CCD MARMOSAIC 225 mm CCD 2003-10-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-ID 1.00 APS 22-ID
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 1.16 36 87.7 0.074 0.074 38.6 6.3 168938 168938 9.6
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 1.16 1.2 61.8 0.347 0.347 3.3 5.1 11874
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 MIR THROUGHOUT 1.16 36 168938 168938 8508 87.69 0.15 0.15 0.149 0.1739 0.165 0.1879 RANDOM 11.659
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] 0.44 -0.39 -0.27 -0.48
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 5.401 r_scangle_it 1.793 r_sphericity_free 1.269 r_angle_refined_deg 1.175 r_sphericity_bonded 1.159 r_scbond_it 1.119 r_mcangle_it 0.912 r_angle_other_deg 0.847 r_rigid_bond_restr 0.579 r_mcbond_it 0.558
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 5.401 r_scangle_it 1.793 r_sphericity_free 1.269 r_angle_refined_deg 1.175 r_sphericity_bonded 1.159 r_scbond_it 1.119 r_mcangle_it 0.912 r_angle_other_deg 0.847 r_rigid_bond_restr 0.579 r_mcbond_it 0.558 r_symmetry_vdw_other 0.256 r_nbd_other 0.237 r_nbd_refined 0.23 r_symmetry_vdw_refined 0.221 r_xyhbond_nbd_refined 0.108 r_symmetry_hbond_refined 0.094 r_nbtor_other 0.082 r_chiral_restr 0.074 r_bond_refined_d 0.006 r_gen_planes_refined 0.005 r_gen_planes_other 0.004 r_bond_other_d 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4707 Nucleic Acid Atoms Solvent Atoms 625 Heterogen Atoms 52
Software Software Software Name Purpose REFMAC refinement MAR345 data collection SCALEPACK data scaling SHARP phasing