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Structure of a Kluyveromyces lactis protein involved in RNA decay
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold AlphaFold model
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 280 0.1 M sodium citrate pH 5.6, 0.9-1 M Li2SO4 and 0.6 M ammonium sulfate
Crystal Properties Matthews coefficient Solvent content 2.63 53.16
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 76.82 α = 90 b = 76.82 β = 90 c = 174.31 γ = 120
Symmetry Space Group P 32 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 DECTRIS EIGER X 9M 2019-06-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SOLEIL BEAMLINE PROXIMA 2 0.97856 SOLEIL PROXIMA 2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 2.45 43.77 99.8 0.0115 0.999 30.8 59.8 22619
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.45 2.51 100 3.897 0.605 1.1
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 (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 AlphaFold model 2.45 43.76 22619 1131 99.9 0.2314 0.2295 0.2332 0.2687 0.2736 RANDOM 94.56
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] -2.8488 -2.8488 5.6975
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 18.83 t_omega_torsion 2.97 t_angle_deg 0.97 t_bond_d 0.008 t_dihedral_angle_d t_gen_planes t_it t_chiral_improper_torsion t_ideal_dist_contact
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2941 Nucleic Acid Atoms Solvent Atoms 33 Heterogen Atoms 39
Software Software Software Name Purpose BUSTER refinement PDB_EXTRACT data extraction XDS data reduction XSCALE data scaling MOLREP phasing