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Crystal structure of the catalytic core domain of human PHF8
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2YU2 PDB ENTRY 2YU2
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 6.5 298 200mM KCl, 100mM Mes, 20% PEG5K, pH 6.5, VAPOR DIFFUSION, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.14 42.55
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 52.238 α = 90 b = 52.583 β = 90 c = 134.93 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 200 CCD MARMOSAIC 225 mm CCD 2009-05-31 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL17U 0.97939 SSRF BL17U
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 2.4 50 98 0.055 0.06 31 5.7 15300 14988 3 3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.4 2.44 4.1 0.426 0.37 2.6 3.7 616
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 PDB ENTRY 2YU2 2.4 20 14861 14109 752 98.32 0.224 0.222 0.2286 0.261 0.2483 RANDOM 33.634
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] 2.17 -0.41 -1.76
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.369 r_dihedral_angle_4_deg 17.318 r_dihedral_angle_3_deg 15.909 r_dihedral_angle_1_deg 5.328 r_scangle_it 1.318 r_angle_refined_deg 1.019 r_scbond_it 0.807 r_mcangle_it 0.617 r_mcbond_it 0.329 r_chiral_restr 0.07
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.369 r_dihedral_angle_4_deg 17.318 r_dihedral_angle_3_deg 15.909 r_dihedral_angle_1_deg 5.328 r_scangle_it 1.318 r_angle_refined_deg 1.019 r_scbond_it 0.807 r_mcangle_it 0.617 r_mcbond_it 0.329 r_chiral_restr 0.07 r_bond_refined_d 0.007 r_gen_planes_refined 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2648 Nucleic Acid Atoms Solvent Atoms 111 Heterogen Atoms 1
Software Software Software Name Purpose MAR345 data collection PHASER phasing REFMAC refinement DENZO data reduction SCALEPACK data scaling