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CASP8 isoform B DED domain
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details other Internal structure
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8 294 100mM Hepes pH 7.5, 20% Ethylene Glycol, 18% PEG 3350, 200mM Sodium Chloride
Crystal Properties Matthews coefficient Solvent content 2.68 54.13
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 101.418 α = 90 b = 50.414 β = 116.64 c = 52.609 γ = 90
Symmetry Space Group C 1 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 PILATUS 6M 2020-02-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 31-ID 0.9793 APS 31-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.47 47.03 96.6 0.044 12.5 3.3 37049
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.47 1.55 0.414
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 Internal structure 1.47 30 37049 1957 96.25 0.2009 0.1992 0.2015 0.2325 0.2332 RANDOM 25.865
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] -0.02 -0.65 2.88 -1.47
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.196 r_dihedral_angle_4_deg 15.752 r_dihedral_angle_3_deg 14.35 r_dihedral_angle_1_deg 4.881 r_angle_refined_deg 1.297 r_chiral_restr 0.091 r_bond_refined_d 0.009 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1540 Nucleic Acid Atoms Solvent Atoms 235 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction XDS data reduction Aimless data scaling PHASER phasing