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Histone H3 recognition and presentation by the WDR5 module of the MLL1 complex
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1ERJ PDB ENTRY 1ERJ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 Crystals were grown by hanging drop vapour equilibration in Nextal plates as follows: 1 ul of 10 15 mg ml-1 protein solution (10 mM Tris HCl (pH 7.4), 50 mM NaCl, and 10 mM 2-mercaptoethanol) were mixed with 1 ul of well solution composed of 50 mM HEPES (pH 7.5), 100 mM potassium formate, and 10-20% (w/v) polyethylene glycol 3350 and equilibrated at room temperature overnight against 1 ml of well solution.
Crystal Properties Matthews coefficient Solvent content 2.18 43.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 134.257 α = 90 b = 46.336 β = 116.72 c = 111.405 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 Si(111) 2006-02-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 24-ID-C APS 24-ID-C
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 1.88 33.2 99.4 0.091 19.8 6.9 50232 46407 2 2 25.7
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 1.88 1.95 95.1 0.271 6.63 5.4 4776
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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 PDB ENTRY 1ERJ 1.87 33.2 2 48890 46407 2483 96.18 0.17 0.15348 0.1518 0.1519 0.18464 0.1853 RANDOM 17.917
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] -0.88 -0.68 -0.81 1.08
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.906 r_dihedral_angle_4_deg 17.19 r_dihedral_angle_3_deg 12.423 r_dihedral_angle_1_deg 7.062 r_scangle_it 3.414 r_scbond_it 2.208 r_angle_refined_deg 1.373 r_mcangle_it 1.207 r_mcbond_it 0.782 r_nbtor_refined 0.301
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.906 r_dihedral_angle_4_deg 17.19 r_dihedral_angle_3_deg 12.423 r_dihedral_angle_1_deg 7.062 r_scangle_it 3.414 r_scbond_it 2.208 r_angle_refined_deg 1.373 r_mcangle_it 1.207 r_mcbond_it 0.782 r_nbtor_refined 0.301 r_nbd_refined 0.198 r_symmetry_vdw_refined 0.162 r_symmetry_hbond_refined 0.151 r_xyhbond_nbd_refined 0.143 r_chiral_restr 0.102 r_bond_refined_d 0.013 r_gen_planes_refined 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4826 Nucleic Acid Atoms Solvent Atoms 498 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement ADSC data collection HKL-2000 data scaling MOLREP phasing