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Crystal structure of Dot1L in complex with inhibitor CPD11 [N4-methyl-N2-(2-methyl-1-(2-phenoxyphenyl)-1H-indol-6-yl)pyrimidine-2,4-diamine]
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1NW3
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 293 1.4M lithium sulfate
0.1M sodium citrate tribasic dihydrate
0.3M ammonium sulfate
Crystal Properties Matthews coefficient Solvent content 3.51 64.93
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 158.32 α = 90 b = 158.32 β = 90 c = 74.57 γ = 120
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 PSI PILATUS 6M 2014-06-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X10SA 0.99998 SLS X10SA
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 2.3 50 100 0.108 15.82 10.2 47515 49.9
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 2.3 2.36 99.9 1.177 2.33 9.4
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 1nw3 2.3 45.7 47513 2376 99.96 0.1855 0.184 0.1881 0.2131 0.2111 RANDOM 58.16
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] 9.8594 9.8594 -19.7189
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 17.44 t_omega_torsion 3.24 t_angle_deg 1.02 t_bond_d 0.01 t_dihedral_angle_d t_incorr_chiral_ct t_pseud_angle t_trig_c_planes t_gen_planes t_it
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 17.44 t_omega_torsion 3.24 t_angle_deg 1.02 t_bond_d 0.01 t_dihedral_angle_d t_incorr_chiral_ct t_pseud_angle t_trig_c_planes t_gen_planes t_it t_nbd t_improper_torsion t_chiral_improper_torsion t_sum_occupancies t_utility_distance t_utility_angle t_utility_torsion t_ideal_dist_contact
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4998 Nucleic Acid Atoms Solvent Atoms 239 Heterogen Atoms 84
Software Software Software Name Purpose BUSTER refinement XDS data reduction XSCALE data scaling PHASER phasing