☰ Navigation Tabs
D-lyxose isomerasefrom the hyperthermophilic archaeon Thermofilum sp
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 7 293 150 mM Potassium bromide, 30% w/v PEG 2000 MME
Crystal Properties Matthews coefficient Solvent content 2.31 46.8
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 47.77 α = 90 b = 86.91 β = 112.93 c = 54.03 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 2021-03-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.97625 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 1.67 39.26 92.2 0.999 19.4 6.2 43436
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 1.67 1.7 0.326
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 1.67 39.252 43408 2053 92.132 0.181 0.1792 0.1792 0.2107 0.2106 41.016
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] 2.535 0.653 -2.531 -0.409
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.862 r_dihedral_angle_4_deg 16.665 r_dihedral_angle_3_deg 13.972 r_lrange_it 8.334 r_scangle_it 6.553 r_dihedral_angle_1_deg 6.396 r_scbond_it 4.8 r_mcangle_it 4.241 r_mcbond_it 3.34 r_angle_refined_deg 1.612
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.862 r_dihedral_angle_4_deg 16.665 r_dihedral_angle_3_deg 13.972 r_lrange_it 8.334 r_scangle_it 6.553 r_dihedral_angle_1_deg 6.396 r_scbond_it 4.8 r_mcangle_it 4.241 r_mcbond_it 3.34 r_angle_refined_deg 1.612 r_nbtor_refined 0.318 r_nbd_refined 0.208 r_symmetry_nbd_refined 0.194 r_symmetry_xyhbond_nbd_refined 0.158 r_xyhbond_nbd_refined 0.153 r_chiral_restr 0.114 r_ncsr_local_group_1 0.071 r_gen_planes_refined 0.01 r_bond_refined_d 0.009
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2907 Nucleic Acid Atoms Solvent Atoms 247 Heterogen Atoms 46
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling MoRDa phasing