☰ Navigation Tabs
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 2.19 43.92
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 133.473 α = 90 b = 46.521 β = 116.86 c = 112.11 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 mirrors 2006-01-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 5.0.2 0.98720 ALS 5.0.2
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 1.9 43.3 98.9 0.071 16.2 3.2 48816 47173 2 2 25.3
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 1.9 1.97 92.9 0.255 3.82 2.5 4525
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 1.89 43.3 2 47173 44830 2379 94.5 0.162 0.14865 0.14646 0.1458 0.18972 0.1889 RANDOM 18.94
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] -0.59 -0.68 -0.3 0.28
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.127 r_dihedral_angle_4_deg 18.247 r_dihedral_angle_3_deg 12.681 r_dihedral_angle_1_deg 7.185 r_scangle_it 2.756 r_scbond_it 1.716 r_angle_refined_deg 1.261 r_mcangle_it 1.031 r_mcbond_it 0.623 r_nbtor_refined 0.297
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.127 r_dihedral_angle_4_deg 18.247 r_dihedral_angle_3_deg 12.681 r_dihedral_angle_1_deg 7.185 r_scangle_it 2.756 r_scbond_it 1.716 r_angle_refined_deg 1.261 r_mcangle_it 1.031 r_mcbond_it 0.623 r_nbtor_refined 0.297 r_nbd_refined 0.193 r_symmetry_vdw_refined 0.177 r_symmetry_hbond_refined 0.152 r_xyhbond_nbd_refined 0.133 r_chiral_restr 0.086 r_bond_refined_d 0.011 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4875 Nucleic Acid Atoms Solvent Atoms 696 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement ADSC data collection HKL-2000 data scaling CNS phasing