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Crystal structure of the SGF29 in complex with H3K4me3
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3ME9 PDB ENTRY 3ME9
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 291 22% peg3350, 0.1M HEPES. 0.004M trimethylated H3K3 peptide was present in the protein stock solution, pH 7.5, vapor diffusion, hanging drop, temperature 291K
Crystal Properties Matthews coefficient Solvent content 2.07 40.55
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 93.385 α = 90 b = 41.425 β = 121.39 c = 52.527 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 ADSC QUANTUM 315 2009-10-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID 0.97927 APS 19-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 1.26 30 99.9 0.052 9.8 3.5 46388
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.26 1.28 99.1 0.973 2.8 2285
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 PDB ENTRY 3ME9 1.26 20 46365 1445 99.834 0.179 0.178 0.1841 0.2 0.2036 RANDOM 10.384
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] -0.221 -0.133 0.129 -0.047
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 27.965 r_dihedral_angle_4_deg 14.63 r_dihedral_angle_3_deg 11.264 r_dihedral_angle_1_deg 7.329 r_scangle_it 4.51 r_scbond_it 3.189 r_mcangle_it 2.447 r_mcbond_it 1.556 r_angle_refined_deg 1.537 r_rigid_bond_restr 1.246
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 27.965 r_dihedral_angle_4_deg 14.63 r_dihedral_angle_3_deg 11.264 r_dihedral_angle_1_deg 7.329 r_scangle_it 4.51 r_scbond_it 3.189 r_mcangle_it 2.447 r_mcbond_it 1.556 r_angle_refined_deg 1.537 r_rigid_bond_restr 1.246 r_angle_other_deg 0.919 r_mcbond_other 0.437 r_chiral_restr 0.092 r_bond_refined_d 0.016 r_gen_planes_refined 0.008 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1294 Nucleic Acid Atoms Solvent Atoms 156 Heterogen Atoms
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction SBC-Collect data collection HKL-3000 data reduction HKL-3000 data scaling