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Crystal structure of menin reveals the binding site for Mixed Lineage Leukemia (MLL) protein
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6 283 20% PEG 3350, 0.1 M Bis-Tris pH 6.0, 0.2 M ammonium sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 283K
Crystal Properties Matthews coefficient Solvent content 2.2 44.16
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 89.881 α = 90 b = 89.881 β = 90 c = 115.601 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 CCD MARMOSAIC 225 mm CCD mirrors 2011-03-17 M SINGLE WAVELENGTH 2 1 CCD ADSC QUANTUM 210r mirrors 2011-03-17
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-F 0.9787 APS 21-ID-F 2 SYNCHROTRON APS BEAMLINE 19-BM 0.9791 APS 19-BM
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 1.95 50 99.9 0.091 0.091 34.8 13.8 35267 35267 -3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.95 1.98 100 0.78 0.78 3.8 13.5 1725
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 SAD THROUGHOUT 1.95 50 33400 33400 1767 99.95 0.16349 0.16349 0.16107 0.1709 0.21145 0.2147 RANDOM 34.498
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] 0.61 0.61 -1.22
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.129 r_dihedral_angle_4_deg 17.842 r_dihedral_angle_3_deg 13.712 r_dihedral_angle_1_deg 5.894 r_scangle_it 4.012 r_scbond_it 2.621 r_mcangle_it 1.731 r_angle_refined_deg 1.602 r_angle_other_deg 1.001 r_mcbond_it 0.986
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.129 r_dihedral_angle_4_deg 17.842 r_dihedral_angle_3_deg 13.712 r_dihedral_angle_1_deg 5.894 r_scangle_it 4.012 r_scbond_it 2.621 r_mcangle_it 1.731 r_angle_refined_deg 1.602 r_angle_other_deg 1.001 r_mcbond_it 0.986 r_mcbond_other 0.297 r_chiral_restr 0.101 r_bond_refined_d 0.019 r_gen_planes_refined 0.008 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_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3468 Nucleic Acid Atoms Solvent Atoms 339 Heterogen Atoms 6
Software Software Software Name Purpose HKL-3000 data collection MD2 data collection HKL-3000 phasing SHELXD phasing SHELXE model building MLPHARE phasing DM model building RESOLVE model building ARP/wARP model building CCP4 model building REFMAC refinement Coot model building HKL-2000 data reduction HKL-2000 data scaling DM phasing RESOLVE phasing CCP4 phasing