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Crystal structure of Toxoplasma CPSF4-YTH domain bound to m6A
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4R3I
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 4.5 293 50% PEG 400, 0.1M Sodium acetate pH 4.5 and 0.2M LiSO4
Crystal Properties Matthews coefficient Solvent content 2.06 40.25
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 32.474 α = 114.51 b = 35.221 β = 100.436 c = 38.177 γ = 97.766
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 2M 2018-09-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE MASSIF-1 0.9660 ESRF MASSIF-1
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 1.349 30.76 92.64 0.956 6.6 1.6 30036 9.18
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 1.349 1.397 88.38 0.496 2.1 1.7
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 4r3i 1.35 30.76 1.96 30007 1532 92.65 0.1832 0.1825 0.183 0.1967 0.1962 13.21
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 15.8072 f_angle_d 0.8218 f_chiral_restr 0.0774 f_bond_d 0.0053 f_plane_restr 0.0043
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1185 Nucleic Acid Atoms Solvent Atoms 148 Heterogen Atoms 23
Software Software Software Name Purpose DIALS data processing DIALS data scaling PHASER phasing PHENIX model building PHENIX refinement PDB-REDO model building xia2 data reduction DIALS data reduction