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Crystal structure of EHMT2 SET domain in complex with compound 5.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5VSE
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 0.2 M ammonium acetate, 20% PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.48 50.43
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 56.428 α = 90 b = 79.106 β = 91.8 c = 72.527 γ = 90
Symmetry Space Group P 1 21 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 PIXEL RIGAKU HyPix-6000HE 2018-07-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 HF 1.54056
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 2 26.57 98.8 0.068 0.082 0.045 0.998 12.4 3.2 42628
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 2 2.05 91.4 0.845 1.023 0.567 0.738 2.8
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 5VSE 2 25 40516 2085 98.72 0.1944 0.1918 0.1948 0.2447 0.2485 RANDOM 36.126
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] -3.34 1.75 1.23 2
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.566 r_dihedral_angle_4_deg 17.199 r_dihedral_angle_3_deg 14.678 r_dihedral_angle_1_deg 6.828 r_angle_refined_deg 1.513 r_chiral_restr 0.099 r_gen_planes_refined 0.007 r_bond_refined_d 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4311 Nucleic Acid Atoms Solvent Atoms 322 Heterogen Atoms 116
Software Software Software Name Purpose Aimless data scaling REFMAC refinement PDB_EXTRACT data extraction Aimless data reduction PHASER phasing