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Crystal structure of phosphoglucose/phosphomannose isomerase from Pyrobaculum aerophilum in complex with 5-phosphoarabinonate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other NATIVE STRUCTURE
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 = 55.8 α = 90 b = 100.85 β = 113.7 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 1.45 36 97.8 0.078 0.078 13.4 2.9 97954 97954 17.1
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 1.45 1.5 94.3 0.462 0.462 1.6 2.5 9407
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 REFINEMENT FROM NATIVE STRUCTURE THROUGHOUT NATIVE STRUCTURE 1.45 36 97736 97736 4866 94.2 0.17 0.17 0.169 0.1707 0.192 0.1929 RANDOM 15.34
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] -0.37 -0.26 -0.04 0.2
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 5.827 r_scangle_it 3.147 r_scbond_it 1.829 r_angle_refined_deg 1.273 r_mcangle_it 1.099 r_angle_other_deg 1.091 r_mcbond_it 0.586 r_symmetry_vdw_other 0.257 r_nbd_other 0.233 r_nbd_refined 0.209
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 5.827 r_scangle_it 3.147 r_scbond_it 1.829 r_angle_refined_deg 1.273 r_mcangle_it 1.099 r_angle_other_deg 1.091 r_mcbond_it 0.586 r_symmetry_vdw_other 0.257 r_nbd_other 0.233 r_nbd_refined 0.209 r_symmetry_hbond_refined 0.144 r_xyhbond_nbd_refined 0.13 r_symmetry_vdw_refined 0.104 r_nbtor_other 0.081 r_chiral_restr 0.079 r_bond_refined_d 0.008 r_gen_planes_refined 0.005 r_bond_other_d 0.002 r_gen_planes_other 0.002 r_dihedral_angle_2_deg r_dihedral_angle_3_deg r_dihedral_angle_4_deg r_nbtor_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_hbond_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4717 Nucleic Acid Atoms Solvent Atoms 439 Heterogen Atoms 67
Software Software Software Name Purpose REFMAC refinement MAR345 data collection SCALEPACK data scaling