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The crystal structure of PWWP domain of human Hepatoma-derived growth factor 2 in complex with H3K79me3 peptide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3EAE pdb entry 3eae
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 293 2.0M ammonium sulfate, 5% isopropanol. Protein was pre-incubated with 5 equivalents of peptide ligand, VAPOR DIFFUSION, temperature 293K
Crystal Properties Matthews coefficient Solvent content 3.1 60
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 74.934 α = 90 b = 74.934 β = 90 c = 41.764 γ = 120
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD ADSC QUANTUM 315 2009-04-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 24-ID-C 0.97944 APS 24-ID-C
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 2.3 40 100 0.085 11.6 10.8 6094
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 2.3 2.34 100 0.466 10.4 313
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT pdb entry 3eae 2.3 37.468 6063 281 99.802 0.236 0.2337 0.276 0.2702 RANDOM 37.022
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] 1.707 0.853 1.707 -2.56
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.778 r_dihedral_angle_4_deg 14.903 r_dihedral_angle_3_deg 13.072 r_dihedral_angle_1_deg 6.758 r_scangle_it 1.708 r_angle_refined_deg 1.173 r_scbond_it 1.079 r_angle_other_deg 0.792 r_mcangle_it 0.783 r_mcbond_it 0.419
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.778 r_dihedral_angle_4_deg 14.903 r_dihedral_angle_3_deg 13.072 r_dihedral_angle_1_deg 6.758 r_scangle_it 1.708 r_angle_refined_deg 1.173 r_scbond_it 1.079 r_angle_other_deg 0.792 r_mcangle_it 0.783 r_mcbond_it 0.419 r_chiral_restr 0.07 r_mcbond_other 0.069 r_bond_refined_d 0.011 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 764 Nucleic Acid Atoms Solvent Atoms 10 Heterogen Atoms 7
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling MOLREP phasing REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data reduction HKL-2000 data scaling