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MLLT3 in complex with compound PFI-6
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other model generated from apo form crystal
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 100 mM Bis-Tris pH=7.0
150 mM AmSO4
Gradient 20-30% PEG3350
Crystal Properties Matthews coefficient Solvent content 2.32 47
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 49.632 α = 90 b = 49.632 β = 90 c = 122.439 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 293 PIXEL DECTRIS EIGER X 9M 2019-09-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 0.92 Diamond I04-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 46 99.78 0.07432 0.07564 0.01379 20.71 27.1 42219
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.26 1.305 1.597 1.672 0.482 1.27
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 1.26 46 40053 2157 99.81 0.19876 0.1975 0.2076 0.22171 0.2352 RANDOM 19.079
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] -1.27 -1.27 2.53
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.365 r_dihedral_angle_4_deg 17.964 r_dihedral_angle_3_deg 12.743 r_dihedral_angle_1_deg 6.575 r_long_range_B_refined 6.24 r_long_range_B_other 5.974 r_scangle_other 4.386 r_scbond_it 2.984 r_scbond_other 2.968 r_mcangle_other 2.491
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.365 r_dihedral_angle_4_deg 17.964 r_dihedral_angle_3_deg 12.743 r_dihedral_angle_1_deg 6.575 r_long_range_B_refined 6.24 r_long_range_B_other 5.974 r_scangle_other 4.386 r_scbond_it 2.984 r_scbond_other 2.968 r_mcangle_other 2.491 r_mcangle_it 2.485 r_angle_refined_deg 1.865 r_mcbond_it 1.648 r_mcbond_other 1.61 r_angle_other_deg 1.443 r_chiral_restr 0.363 r_bond_refined_d 0.014 r_gen_planes_refined 0.012 r_bond_other_d 0.002 r_gen_planes_other 0.002 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 1148 Nucleic Acid Atoms Solvent Atoms 104 Heterogen Atoms 62
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing