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A native form of glucose isomerase collected at room temperature.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1MNZ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 293 0.1M Hepes, 10% PEG 400, 0.05 M Manganese Chloride, 20% Glucose
Crystal Properties Matthews coefficient Solvent content 2.79 55.88
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 94.074 α = 90 b = 99.225 β = 90 c = 103.034 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 293 PIXEL DECTRIS PILATUS 6M 2015-02-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I02 0.9795 Diamond I02
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 2 69.47 99.8 0.051 18 4.5 32817
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 2 2.1 99.7 0.086 12.9 4.6
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 1MNZ 2 69.47 31116 1701 99.64 0.10769 0.10585 0.1059 0.13985 0.1404 RANDOM 18.462
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] 0.05 0.48 -0.53
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.538 r_dihedral_angle_4_deg 18.218 r_dihedral_angle_3_deg 12.667 r_long_range_B_refined 7.482 r_long_range_B_other 7.481 r_scangle_other 5.541 r_dihedral_angle_1_deg 5.391 r_scbond_it 3.548 r_scbond_other 3.541 r_mcangle_other 2.929
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.538 r_dihedral_angle_4_deg 18.218 r_dihedral_angle_3_deg 12.667 r_long_range_B_refined 7.482 r_long_range_B_other 7.481 r_scangle_other 5.541 r_dihedral_angle_1_deg 5.391 r_scbond_it 3.548 r_scbond_other 3.541 r_mcangle_other 2.929 r_mcangle_it 2.922 r_angle_refined_deg 2.109 r_mcbond_other 2.009 r_mcbond_it 2.008 r_angle_other_deg 1.144 r_chiral_restr 0.136 r_bond_refined_d 0.022 r_gen_planes_refined 0.012 r_bond_other_d 0.002 r_gen_planes_other 0.002 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 3045 Nucleic Acid Atoms Solvent Atoms 301 Heterogen Atoms 26
Software Software Software Name Purpose REFMAC refinement xia2 data reduction xia2 data scaling MOLREP phasing