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Crystal Structure of Glucose Isomerase Soaked with Glucose
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5Y4I
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293.5 PEG 400, MgCl2
Crystal Properties Matthews coefficient Solvent content 2.7 54.48
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 92.505 α = 90 b = 97.82 β = 90 c = 102.297 γ = 90
Symmetry Space Group I 2 2 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 270 2017-09-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PAL/PLS BEAMLINE 7A (6B, 6C1) 0.987 PAL/PLS 7A (6B, 6C1)
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 1.4 70.7 96 0.111 0.125 0.57 24.4 4.8 90913
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.4 1.42 100 0.357 0.4 0.178 0.901 4.79 4.9
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 5Y4I 1.4 70.7 86237 4675 99.42 0.15148 0.15072 0.1592 0.16529 0.172 RANDOM 12.583
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] -0.34 0.62 -0.28
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.171 r_dihedral_angle_4_deg 17.528 r_dihedral_angle_3_deg 11.592 r_dihedral_angle_1_deg 5.55 r_long_range_B_refined 5.355 r_long_range_B_other 4.83 r_scangle_other 3.435 r_scbond_it 2.244 r_scbond_other 2.244 r_angle_refined_deg 2.041
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.171 r_dihedral_angle_4_deg 17.528 r_dihedral_angle_3_deg 11.592 r_dihedral_angle_1_deg 5.55 r_long_range_B_refined 5.355 r_long_range_B_other 4.83 r_scangle_other 3.435 r_scbond_it 2.244 r_scbond_other 2.244 r_angle_refined_deg 2.041 r_mcangle_other 1.749 r_mcangle_it 1.735 r_mcbond_it 1.275 r_mcbond_other 1.18 r_angle_other_deg 0.924 r_chiral_restr 0.118 r_bond_refined_d 0.022 r_gen_planes_refined 0.012 r_bond_other_d 0.001 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 r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3022 Nucleic Acid Atoms Solvent Atoms 522 Heterogen Atoms 5
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing