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The 1.03 angstrom structure (P212121) of glucose isomerase crystallized in high-strength agarose hydrogel
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1O1H
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 MICROBATCH 7.5 293 0.1 M Hepes-NaOH (pH 7.5), 1.75 M (NH4)2SO4
Crystal Properties Matthews coefficient Solvent content 2.3 46.47
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 94.082 α = 90 b = 98.285 β = 90 c = 85.777 γ = 90
Symmetry Space Group P 21 21 2
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 ADSC QUANTUM 315 2008-09-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL44XU 0.90 SPring-8 BL44XU
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 1.03 50 99.2 0.057 9.1 3.6 386570
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 1.03 1.07 99.8 0.407 1.9 3.5
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) 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 1O1H 1.03 50 367026 16000 99.19 0.1286 0.12748 0.1288 0.14969 0.1504 RANDOM 10.697
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] 0.58 -0.29 -0.29
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.478 r_sphericity_free 19.816 r_dihedral_angle_4_deg 15.552 r_dihedral_angle_3_deg 11.579 r_rigid_bond_restr 8.439 r_sphericity_bonded 6.062 r_dihedral_angle_1_deg 5.807 r_long_range_B_refined 2.74 r_scangle_other 2.722 r_long_range_B_other 2.463
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.478 r_sphericity_free 19.816 r_dihedral_angle_4_deg 15.552 r_dihedral_angle_3_deg 11.579 r_rigid_bond_restr 8.439 r_sphericity_bonded 6.062 r_dihedral_angle_1_deg 5.807 r_long_range_B_refined 2.74 r_scangle_other 2.722 r_long_range_B_other 2.463 r_scbond_it 2.132 r_scbond_other 2.063 r_angle_refined_deg 2.037 r_mcbond_it 1.907 r_mcangle_other 1.863 r_mcangle_it 1.862 r_mcbond_other 1.651 r_angle_other_deg 0.941 r_chiral_restr 0.129 r_bond_refined_d 0.022 r_gen_planes_refined 0.014 r_bond_other_d 0.002 r_gen_planes_other 0.001 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_scangle_it
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6092 Nucleic Acid Atoms Solvent Atoms 1058 Heterogen Atoms 24
Software Software Software Name Purpose REFMAC refinement DENZO data reduction HKL-2000 data scaling MOLREP phasing