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Crystal Structure of NSD3 tandem PHD5-C5HCH domains complexed with H3 peptide 1-15
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4GNE
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 283 0.1M Hepes pH 7.5, 70% v/v MPD, VAPOR DIFFUSION, HANGING DROP, temperature 283K
Crystal Properties Matthews coefficient Solvent content 2.17 43.33
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 60.03 α = 90 b = 62.71 β = 90 c = 62.84 γ = 90
Symmetry Space Group I 2 2 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 CCD ADSC QUANTUM 315r 2011-11-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL17U 0.97838 SSRF BL17U
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 1.55 44.389 99.8 0.064 13.2 6.8 17558 17540 2 2
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Rrim I (All) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.55 1.63 100 0.423 0.423 0.457 0.173 1.8 6.9 2531
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) 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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 4GNE 1.55 21.7 17558 17533 890 99.68 0.1625 0.1602 0.1616 0.2046 0.2062 RANDOM 30.9116
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] -0.03 -0.12 0.15
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.062 r_sphericity_bonded 19.455 r_dihedral_angle_3_deg 13.802 r_dihedral_angle_4_deg 10.529 r_dihedral_angle_1_deg 5.91 r_rigid_bond_restr 3.495 r_angle_refined_deg 1.314 r_chiral_restr 0.078 r_bond_refined_d 0.008 r_gen_planes_refined 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 815 Nucleic Acid Atoms Solvent Atoms 98 Heterogen Atoms 4
Software Software Software Name Purpose MOSFLM data reduction SCALA data scaling MOLREP phasing REFMAC refinement PDB_EXTRACT data extraction ADSC data collection