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Crystal structure of glucose isomerase from Streptomyces rubiginosus
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1XIB
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 293 0.1 M CaCl2, 16-22% MPD (v/v) and 0.1 M Tris-HCl pH 7.0
Crystal Properties Matthews coefficient Solvent content 2.7 54.41
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 92.854 α = 90 b = 98.061 β = 90 c = 102.279 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 SBC-3 2001-01-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID 0.9792, 1.5406 APS 19-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Rpim I (All) 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 1.7 50.01 96.2 0.013 1 125 43.1 49609 -3
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 FOURIER SYNTHESIS THROUGHOUT 1XIB 1.7 38.9 48877 2547 99.08 0.11988 0.11877 0.1327 0.14161 0.1524 RANDOM 10.813
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] -0.16 0.43 -0.28
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 26.983 r_dihedral_angle_4_deg 16.483 r_dihedral_angle_3_deg 12.02 r_dihedral_angle_1_deg 5.441 r_long_range_B_refined 4.657 r_long_range_B_other 4.054 r_scangle_other 1.812 r_angle_refined_deg 1.333 r_scbond_it 1.122 r_scbond_other 1.122
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 26.983 r_dihedral_angle_4_deg 16.483 r_dihedral_angle_3_deg 12.02 r_dihedral_angle_1_deg 5.441 r_long_range_B_refined 4.657 r_long_range_B_other 4.054 r_scangle_other 1.812 r_angle_refined_deg 1.333 r_scbond_it 1.122 r_scbond_other 1.122 r_mcangle_it 0.971 r_mcangle_other 0.964 r_mcbond_it 0.587 r_mcbond_other 0.587 r_angle_other_deg 0.495 r_chiral_restr 0.065 r_bond_refined_d 0.007 r_gen_planes_refined 0.007 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 3046 Nucleic Acid Atoms Solvent Atoms 489 Heterogen Atoms 25
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-3000 data scaling REFMAC phasing