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menin mutant M327I in complex with MLL peptide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4GQ6
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 285 0.2 M lithium sulfate, 0.1 M HEPES, pH 7.5, 25% (w/v) PEG-3,350
Crystal Properties Matthews coefficient Solvent content 2.21 44.3
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 49.075 α = 90 b = 80.456 β = 90 c = 124.946 γ = 90
Symmetry Space Group P 21 21 21
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 MARMOSAIC 300 mm CCD 2023-04-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-G 0.97857 APS 21-ID-G
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 1.46 50 99.5 0.082 28.13 7 86122
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 1.46 1.49 97.1 0.726 2.27
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1.461 31.131 86049 4372 99.468 0.157 0.1557 0.1566 0.1844 0.1847 17.426
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] 0.377 0.851 -1.229
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.387 r_dihedral_angle_3_deg 11.074 r_dihedral_angle_2_deg 10.028 r_dihedral_angle_1_deg 6.089 r_lrange_it 5.67 r_lrange_other 5.669 r_scangle_it 4.315 r_scangle_other 4.314 r_scbond_it 2.891 r_scbond_other 2.89
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.387 r_dihedral_angle_3_deg 11.074 r_dihedral_angle_2_deg 10.028 r_dihedral_angle_1_deg 6.089 r_lrange_it 5.67 r_lrange_other 5.669 r_scangle_it 4.315 r_scangle_other 4.314 r_scbond_it 2.891 r_scbond_other 2.89 r_mcangle_other 2.738 r_mcangle_it 2.737 r_angle_refined_deg 1.995 r_mcbond_it 1.873 r_mcbond_other 1.873 r_angle_other_deg 0.68 r_symmetry_nbd_refined 0.324 r_nbd_refined 0.236 r_nbd_other 0.223 r_nbtor_refined 0.185 r_symmetry_nbd_other 0.178 r_symmetry_xyhbond_nbd_refined 0.172 r_xyhbond_nbd_refined 0.159 r_chiral_restr 0.104 r_dihedral_angle_other_2_deg 0.079 r_symmetry_nbtor_other 0.079 r_bond_refined_d 0.012 r_gen_planes_refined 0.01 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3738 Nucleic Acid Atoms Solvent Atoms 533 Heterogen Atoms 44
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing