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Crystal structure of Toxoplasma CPSF4-YTH domain in apo form
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 5.6 293 20 % PEG 4000, 20% isopropanol and 0.1M tri-sodium citrate pH 5.6
Crystal Properties Matthews coefficient Solvent content 2.22 44.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 40.18 α = 90 b = 40.18 β = 90 c = 202.6 γ = 90
Symmetry Space Group P 41 21 2
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 16M 2019-12-13 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 1.23 34.53 99.32 1 20.3 11 49444 16.7
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 1.23 1.274 93.7 0.427 1 4.3
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 1.23 34.53 1.34 49441 2500 99.33 0.1781 0.1767 0.173 0.2038 0.1969 22.56
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 14.5699 f_angle_d 0.7709 f_chiral_restr 0.0789 f_plane_restr 0.0049 f_bond_d 0.0046
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1236 Nucleic Acid Atoms Solvent Atoms 150 Heterogen Atoms 4
Software Software Software Name Purpose DIALS data scaling PHENIX data reduction PHASER phasing PHENIX model building PHENIX refinement PDB-REDO model building