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High resolution crystal structure of Glucose Isomerase from Streptomyces sp. SK
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1MUW
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 7 298 PEG 3350, Mg acetate, pH 7, VAPOR DIFFUSION, temperature 298.0K
Crystal Properties Matthews coefficient Solvent content 2.17 43.35
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 110.8 α = 90 b = 91.68 β = 119.65 c = 84.61 γ = 90
Symmetry Space Group C 1 2 1
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 PSI PILATUS 6M 2011-11-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 0.97946 ESRF ID23-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 1.73 48.14 96.4 5.8 13 3.7 77187 74395 1 1
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.73 1.9 93.4
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) 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 1MUW 1.73 48.14 70674 70674 3720 100 0.13378 0.13094 0.1319 0.18786 0.1887 RANDOM 26.68
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] 0.15 0.62 0.15 0.31
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.177 r_dihedral_angle_4_deg 17.008 r_dihedral_angle_3_deg 13.411 r_scangle_it 7.236 r_scbond_it 4.998 r_dihedral_angle_1_deg 4.941 r_mcangle_it 3.055 r_rigid_bond_restr 2.608 r_mcbond_it 1.996 r_angle_refined_deg 1.795
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.177 r_dihedral_angle_4_deg 17.008 r_dihedral_angle_3_deg 13.411 r_scangle_it 7.236 r_scbond_it 4.998 r_dihedral_angle_1_deg 4.941 r_mcangle_it 3.055 r_rigid_bond_restr 2.608 r_mcbond_it 1.996 r_angle_refined_deg 1.795 r_chiral_restr 0.144 r_bond_refined_d 0.024 r_gen_planes_refined 0.011 r_bond_other_d r_angle_other_deg r_gen_planes_other 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_mcbond_other r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6036 Nucleic Acid Atoms Solvent Atoms 366 Heterogen Atoms 57
Software Software Software Name Purpose ADSC data collection BALBES phasing REFMAC refinement XDS data reduction XSCALE data scaling