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D-lyxose isomerase from the hyperthermophilic archaeon Thermofilum sp complexed with D-mannose
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 6 291 100 mM SPG ph 6.0, 25% w/v PEG 1500,
40 mM D-mannose
Crystal Properties Matthews coefficient Solvent content 2.46 49.91
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 47.909 α = 90 b = 121.013 β = 90 c = 70.537 γ = 90
Symmetry Space Group C 2 2 21
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 2019-12-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.9795 Diamond I04
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 1.57 37.692 99.9 0.997 6.6 5.2 29074
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 1.57 1.6 0.277
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 1.57 37.692 29036 1439 99.852 0.178 0.1755 0.1755 0.2176 0.2176 25.025
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] 0.497 -0.034 -0.463
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.469 r_dihedral_angle_4_deg 16.376 r_dihedral_angle_3_deg 15.136 r_dihedral_angle_1_deg 6.74 r_lrange_it 6.582 r_scangle_it 4.155 r_scbond_it 3.003 r_mcangle_it 2.648 r_mcbond_it 1.882 r_angle_refined_deg 1.736
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.469 r_dihedral_angle_4_deg 16.376 r_dihedral_angle_3_deg 15.136 r_dihedral_angle_1_deg 6.74 r_lrange_it 6.582 r_scangle_it 4.155 r_scbond_it 3.003 r_mcangle_it 2.648 r_mcbond_it 1.882 r_angle_refined_deg 1.736 r_nbtor_refined 0.319 r_symmetry_nbd_refined 0.262 r_nbd_refined 0.206 r_symmetry_xyhbond_nbd_refined 0.165 r_xyhbond_nbd_refined 0.143 r_chiral_restr 0.114 r_gen_planes_refined 0.01 r_bond_refined_d 0.009
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1464 Nucleic Acid Atoms Solvent Atoms 224 Heterogen Atoms 33
Software Software Software Name Purpose REFMAC refinement DIALS data reduction Aimless data scaling MoRDa phasing