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X-ray structure of WDR5delta24 bound to the Kaposi's sarcoma herpesvirus LANA win motif peptide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4ERY
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.5 294 100 mM Bis-Tris pH 5.5, 50 mM (NH4)2SO4, 25% PEG3350
Crystal Properties Matthews coefficient Solvent content 1.94 36.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 46.313 α = 72.579 b = 53.171 β = 89.749 c = 65.124 γ = 73.156
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 6M Vertical CRL / Horizontal Eliptical mirror 2017-04-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID30B 0.9762 ESRF ID30B
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) R Split (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 1.4996 61.9364 86.35 0.068 0.082 0.046 0.993 0.069 7.8 3.1 78054 13.72
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) R Split (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.5 1.53 87.4 0.38 0.461 0.258 0.816 0.381 2.1 3.1
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 4ery 1.5 39 1.97 78022 3891 86.18 0.1949 0.1932 0.1946 0.2268 0.2272 17.1
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 7.5103 f_angle_d 1.1561 f_chiral_restr 0.0708 f_bond_d 0.0105 f_plane_restr 0.0089
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4713 Nucleic Acid Atoms Solvent Atoms 692 Heterogen Atoms
Software Software Software Name Purpose PHENIX refinement DIALS data reduction Aimless data scaling MOLREP phasing