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Crystal structure of PHF1 in complex with H3K36me3 substitution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4HCZ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 4.6 291 1.2 M ammonium sulfate and 0.1 M sodium acetate 4.6
Crystal Properties Matthews coefficient Solvent content 2.17 43.4
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 153.003 α = 90 b = 65.616 β = 97.122 c = 29.026 γ = 90
Symmetry Space Group C 1 2 1
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 RIGAKU SATURN A200 2016-06-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU FR-E SUPERBRIGHT 1.54
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) 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 1.7 40.07 93.8 0.048 0.056 0.029 0.998 16.4 3.7 29381
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) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.7 1.73 90.9 0.416 0.487 0.251 0.81 3.6
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 4HCZ 1.7 32.802 29359 1455 93.42 0.199 0.197 0.2106 0.2407 0.2498 18.886
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] 0.098 0.025 0.766 -0.844
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.638 r_dihedral_angle_4_deg 13.449 r_dihedral_angle_3_deg 12.48 r_dihedral_angle_1_deg 7.147 r_lrange_it 4.533 r_lrange_other 4.423 r_scangle_other 3.17 r_scangle_it 3.166 r_mcangle_other 2.585 r_mcangle_it 2.584
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.638 r_dihedral_angle_4_deg 13.449 r_dihedral_angle_3_deg 12.48 r_dihedral_angle_1_deg 7.147 r_lrange_it 4.533 r_lrange_other 4.423 r_scangle_other 3.17 r_scangle_it 3.166 r_mcangle_other 2.585 r_mcangle_it 2.584 r_scbond_it 2.106 r_scbond_other 2.092 r_mcbond_it 1.708 r_mcbond_other 1.703 r_angle_refined_deg 1.664 r_angle_other_deg 1.305 r_symmetry_nbd_refined 0.305 r_nbd_refined 0.228 r_nbd_other 0.201 r_symmetry_nbd_other 0.189 r_nbtor_refined 0.167 r_symmetry_xyhbond_nbd_refined 0.149 r_xyhbond_nbd_refined 0.145 r_symmetry_nbtor_other 0.079 r_chiral_restr 0.064 r_bond_refined_d 0.011 r_gen_planes_refined 0.009 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2152 Nucleic Acid Atoms Solvent Atoms 114 Heterogen Atoms 49
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PDB_EXTRACT data extraction XDS data reduction PHASER phasing