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Menin in complex with MI-273
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4GPQ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8 283 0.2 M ammonium acetate, 0.1 M HEPES and 25% w/v PEG 3,350. This solution was mixed 1:1 with 2.5mg/mL protein in 50mM Tris-HCl, 50mM NaCl, and 1mM TCEP. Prior to data collection, crystals were transferred into a cryo-solution containing 20% PEG550 MME and flash-frozen in liquid nitrogen
Crystal Properties Matthews coefficient Solvent content 2.23 44.85
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 48.553 α = 90 b = 80.189 β = 90 c = 124.989 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 2012-08-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-D 0.97928 APS 21-ID-D
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 1.66 50 99.5 0.116 7.2 5.9 58205
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 1.66 1.69 97.2 0.783 5.4 2806
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 4GPQ 1.66 49.34 55111 2934 99.18 0.1591 0.1575 0.1692 0.1884 0.1977 RANDOM 19.443
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] 0.85 -0.04 -0.8
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.738 r_dihedral_angle_4_deg 16.885 r_dihedral_angle_3_deg 11.681 r_dihedral_angle_1_deg 5.495 r_mcangle_it 5.392 r_mcbond_it 4.339 r_mcbond_other 4.338 r_angle_other_deg 3.647 r_angle_refined_deg 1.828 r_chiral_restr 0.119
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.738 r_dihedral_angle_4_deg 16.885 r_dihedral_angle_3_deg 11.681 r_dihedral_angle_1_deg 5.495 r_mcangle_it 5.392 r_mcbond_it 4.339 r_mcbond_other 4.338 r_angle_other_deg 3.647 r_angle_refined_deg 1.828 r_chiral_restr 0.119 r_gen_planes_other 0.02 r_bond_refined_d 0.017 r_gen_planes_refined 0.01 r_bond_other_d
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3618 Nucleic Acid Atoms Solvent Atoms 455 Heterogen Atoms 80
Software Software Software Name Purpose HKL-2000 data scaling REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data reduction MOLREP phasing