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Crystal structure of ENL (MLLT1), apo form
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 293.15 30% PEG 2000MME, 0.1M KBr
Crystal Properties Matthews coefficient Solvent content 2.14 42.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 49.419 α = 90 b = 49.419 β = 90 c = 128.31 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 1.81 46.12 100 0.09 0.028 0.998 14.3 11.9 15436 27.4
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 1.81 1.84 99.8 0.841 0.286 0.768 3.2 10.2
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 5j9s 1.81 39.18 14612 757 99.97 0.19369 0.1915 0.2007 0.23661 0.2426 RANDOM 33.092
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] -1.43 -1.43 2.86
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.535 r_dihedral_angle_4_deg 18.919 r_dihedral_angle_3_deg 13.931 r_long_range_B_refined 7.359 r_long_range_B_other 7.358 r_dihedral_angle_1_deg 6.528 r_scangle_other 4.516 r_mcangle_it 3.217 r_mcangle_other 3.215 r_scbond_it 2.898
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.535 r_dihedral_angle_4_deg 18.919 r_dihedral_angle_3_deg 13.931 r_long_range_B_refined 7.359 r_long_range_B_other 7.358 r_dihedral_angle_1_deg 6.528 r_scangle_other 4.516 r_mcangle_it 3.217 r_mcangle_other 3.215 r_scbond_it 2.898 r_scbond_other 2.896 r_mcbond_other 2.026 r_mcbond_it 2.024 r_angle_refined_deg 1.459 r_angle_other_deg 1.296 r_chiral_restr 0.072 r_bond_refined_d 0.015 r_gen_planes_refined 0.011 r_bond_other_d 0.001 r_gen_planes_other 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 1155 Nucleic Acid Atoms Solvent Atoms 82 Heterogen Atoms 20
Software Software Software Name Purpose REFMAC refinement iMOSFLM data reduction Aimless data scaling PHASER phasing