☰ Navigation Tabs
Crystal structure of Eed in complex with a trimethylated histone H1K26 peptide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other SeMet Eed Structure
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 291 4M Sodium formate, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 2.59 52.44
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 57.573 α = 90 b = 85.18 β = 90 c = 91.352 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 100 IMAGE PLATE RIGAKU RAXIS IV++ M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 HF 1.5418
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 2.65 30 98.1 0.119 0.119 11.3 4.2 12915 12915 2
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) 2.65 2.74 98.8 0.389 0.389 3.2 4
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 (All) 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 SeMet Eed Structure 2.65 30 12670 12670 659 98.24 0.18418 0.18418 0.18036 0.1719 0.25924 0.2443 RANDOM 17.696
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] 0.14 -1.32 1.18
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.391 r_dihedral_angle_4_deg 16.19 r_dihedral_angle_3_deg 15.05 r_dihedral_angle_1_deg 6.442 r_scangle_it 1.876 r_angle_refined_deg 1.215 r_scbond_it 1.085 r_mcangle_it 0.914 r_mcbond_it 0.498 r_nbtor_refined 0.305
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.391 r_dihedral_angle_4_deg 16.19 r_dihedral_angle_3_deg 15.05 r_dihedral_angle_1_deg 6.442 r_scangle_it 1.876 r_angle_refined_deg 1.215 r_scbond_it 1.085 r_mcangle_it 0.914 r_mcbond_it 0.498 r_nbtor_refined 0.305 r_symmetry_hbond_refined 0.235 r_nbd_refined 0.189 r_symmetry_vdw_refined 0.182 r_xyhbond_nbd_refined 0.141 r_chiral_restr 0.085 r_bond_refined_d 0.009 r_gen_planes_refined 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3000 Nucleic Acid Atoms Solvent Atoms 166 Heterogen Atoms
Software Software Software Name Purpose HKL-2000 data collection AMoRE phasing REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling