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Crystal structure of DmCfp1 PHD finger bound to H3K4me3
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5WLE
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 295 15% PEG3350, 0.01M Tris pH8.5, 0.2M Ammonium sulfate
Crystal Properties Matthews coefficient Solvent content 1.8 31.69
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 33.27 α = 90 b = 43.12 β = 90 c = 47.56 γ = 90
Symmetry Space Group P 21 21 21
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 2024-03-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-D 1.0 APS 21-ID-D
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 1.53 31.95 99.46 0.134 0.14 0.039 11.6 12.8 10748 16.2
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.53 1.585 98.87 1.372 1.425 0.381 2.1 13.6
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 1.53 31.95 1.34 10746 548 99.46 0.158 0.1562 0.1562 0.1936 0.1935 23.29
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 6.0388 f_angle_d 0.7132 f_chiral_restr 0.0491 f_plane_restr 0.005 f_bond_d 0.0038
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 582 Nucleic Acid Atoms Solvent Atoms 70 Heterogen Atoms 17
Software Software Software Name Purpose PHENIX refinement Aimless data scaling PHASER phasing xia2 data reduction Coot model building