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Subatomic crystal structure of glucose isomerase from Streptomyces rubiginosus
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7CJP
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 295 Tris-HCl, pH 8.0, PEG400, MgCl2
Crystal Properties Matthews coefficient Solvent content 2.72 54.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 92.675 α = 90 b = 98.626 β = 90 c = 102.137 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 PIXEL DECTRIS PILATUS 6M 2021-12-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PAL/PLS BEAMLINE 11C 0.8265 PAL/PLS 11C
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) CC (Half) 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 0.99 40.77 99.5 0.999 12.2 6.1 255970
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 0.99 1.01 94.6 0.561
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 0.99 40.77 243532 12883 99.5 0.15874 0.15812 0.1596 0.17071 0.1714 RANDOM 10.999
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] 0.01 0.42 -0.43
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.957 r_dihedral_angle_4_deg 13.805 r_dihedral_angle_3_deg 11.187 r_dihedral_angle_1_deg 6.098 r_long_range_B_refined 4.745 r_long_range_B_other 4.383 r_scangle_other 3.397 r_scbond_it 2.306 r_scbond_other 2.306 r_angle_refined_deg 2.043
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.957 r_dihedral_angle_4_deg 13.805 r_dihedral_angle_3_deg 11.187 r_dihedral_angle_1_deg 6.098 r_long_range_B_refined 4.745 r_long_range_B_other 4.383 r_scangle_other 3.397 r_scbond_it 2.306 r_scbond_other 2.306 r_angle_refined_deg 2.043 r_angle_other_deg 1.677 r_mcangle_other 1.285 r_mcangle_it 1.277 r_mcbond_it 0.943 r_mcbond_other 0.907 r_chiral_restr 0.12 r_bond_refined_d 0.018 r_gen_planes_refined 0.013 r_gen_planes_other 0.002 r_bond_other_d 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 3033 Nucleic Acid Atoms Solvent Atoms 502 Heterogen Atoms 13
Software Software Software Name Purpose REFMAC refinement xia2 data reduction xia2 data scaling MOLREP phasing