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Ancestral glycosidase (family 1)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2J78
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 HR1 (#C41): 0.1 M HEPES Na pH 7.5, 10% v/v 2-Propanol, 20% w/v PEG 4,000
Crystal Properties Matthews coefficient Solvent content 1.97 37.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 52.263 α = 90 b = 80.668 β = 100.061 c = 97.808 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 PILATUS3 6M 2019-06-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALBA BEAMLINE XALOC 0.9793 ALBA XALOC
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 2.5 48.15 99.7 0.999 10.9 7.4 27987 59.93
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 2.5 2.59 97.4 0.707 1.7 7.5
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2J78 2.5 48.15 1.34 27818 1405 99.94 0.1964 0.1939 0.1976 0.243 0.2456 76.5
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 6.1312 f_angle_d 0.6626 f_chiral_restr 0.045 f_plane_restr 0.0036 f_bond_d 0.0034
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6156 Nucleic Acid Atoms Solvent Atoms 34 Heterogen Atoms 176
Software Software Software Name Purpose MxCuBE data collection PHENIX refinement XDS data reduction Aimless data scaling Coot model building