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D-lyxose isomerase from the hyperthermophilic archaeon Thermofilum sp complexed with D-fructose
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2Y0O
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 MICROBATCH 5.5 291 200 mM ammonium acetate, 100 mM Bis-Tris pH 5.5, 25 % w/v PEG 3350, 15 mM fructose
Crystal Properties Matthews coefficient Solvent content 2.38 48.25
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 46.958 α = 90 b = 86.647 β = 112.274 c = 53.837 γ = 90
Symmetry Space Group P 1 21 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 DECTRIS EIGER2 XE 16M 2020-10-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.9763 Diamond I03
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 1.345 86.65 100 0.999 14.9 13.4 88231
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 1.345 1.37 0.333
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2y0o 1.345 49.819 88130 4293 99.906 0.185 0.1837 0.1837 0.2126 0.2127 34.936
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] 2.019 0.367 -1.609 -0.532
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.964 r_dihedral_angle_4_deg 18.687 r_dihedral_angle_3_deg 14.443 r_lrange_it 8.368 r_dihedral_angle_1_deg 6.583 r_scangle_it 5.666 r_mcangle_it 4.235 r_scbond_it 3.906 r_mcbond_it 2.912 r_angle_refined_deg 1.838
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.964 r_dihedral_angle_4_deg 18.687 r_dihedral_angle_3_deg 14.443 r_lrange_it 8.368 r_dihedral_angle_1_deg 6.583 r_scangle_it 5.666 r_mcangle_it 4.235 r_scbond_it 3.906 r_mcbond_it 2.912 r_angle_refined_deg 1.838 r_nbtor_refined 0.319 r_symmetry_xyhbond_nbd_refined 0.229 r_nbd_refined 0.215 r_symmetry_nbd_refined 0.211 r_xyhbond_nbd_refined 0.149 r_chiral_restr 0.107 r_ncsr_local_group_1 0.096 r_gen_planes_refined 0.011 r_bond_refined_d 0.01
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3001 Nucleic Acid Atoms Solvent Atoms 340 Heterogen Atoms 38
Software Software Software Name Purpose REFMAC refinement DIALS data reduction Aimless data scaling MoRDa phasing