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Crystal structure of ENL (MLLT1) in complex with compound 12
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5J9S
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.5 293.15 25% PEG 3350, 0.2M ammonium sulfate, 0.1M bis-tris, pH 5.5
Crystal Properties Matthews coefficient Solvent content 2.18 43.55
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 49.039 α = 90 b = 49.039 β = 90 c = 132.729 γ = 90
Symmetry Space Group P 43 21 2
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 DECTRIS PILATUS3 6M 2018-07-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.97950 Diamond I04
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) 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 66.39 100 0.079 0.03 0.996 15.7 8.6 11691 29.3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2 2.05 100 0.216 0.08 0.987 7.7 8.9
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 5j9s 2 46 10967 577 99.24 0.219 0.21689 0.26031 0.2885 RANDOM 36.577
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] -2.57 -2.57 5.13
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.038 r_dihedral_angle_4_deg 25.472 r_dihedral_angle_3_deg 12.806 r_dihedral_angle_1_deg 7.125 r_long_range_B_refined 7.05 r_long_range_B_other 7.048 r_scangle_other 3.199 r_mcangle_it 2.431 r_mcangle_other 2.43 r_scbond_it 1.993
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.038 r_dihedral_angle_4_deg 25.472 r_dihedral_angle_3_deg 12.806 r_dihedral_angle_1_deg 7.125 r_long_range_B_refined 7.05 r_long_range_B_other 7.048 r_scangle_other 3.199 r_mcangle_it 2.431 r_mcangle_other 2.43 r_scbond_it 1.993 r_scbond_other 1.991 r_mcbond_it 1.523 r_mcbond_other 1.514 r_angle_refined_deg 1.434 r_angle_other_deg 1.177 r_chiral_restr 0.072 r_bond_refined_d 0.013 r_gen_planes_refined 0.01 r_gen_planes_other 0.002 r_bond_other_d 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1169 Nucleic Acid Atoms Solvent Atoms 62 Heterogen Atoms 41
Software Software Software Name Purpose REFMAC refinement iMOSFLM data reduction Aimless data scaling PHASER phasing