☰ Navigation Tabs
Human menin with bound inhibitor MIV-4
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4GPQ pdb entry 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 pH 7.5 and 25% w/v PEG 3,350. This solution was mixed 1:1 with 2.5mg/mL protein in 50mM Tris-HCl (pH 8.0), 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, VAPOR DIFFUSION, SITTING DROP, temperature 283K
Crystal Properties Matthews coefficient Solvent content 2.21 44.39
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 48.568 α = 90 b = 79.865 β = 90 c = 124.464 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 CCD MARMOSAIC 225 mm CCD 2012-08-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-F 0.97872 APS 21-ID-F
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 1.49 38.02 98.5 0.069 28.38 6.6 368758 74065
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) 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 pdb entry 4GPQ 1.49 38.02 74065 70287 3701 92.71 0.16202 0.16062 0.1651 0.18819 0.1901 RANDOM 19.977
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] 0.09 -0.26 0.17
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.593 r_dihedral_angle_4_deg 16.134 r_dihedral_angle_3_deg 12.063 r_long_range_B_refined 8.093 r_long_range_B_other 8.092 r_dihedral_angle_1_deg 5.759 r_scangle_other 5.28 r_scbond_it 4.034 r_scbond_other 4.031 r_mcangle_it 3.311
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.593 r_dihedral_angle_4_deg 16.134 r_dihedral_angle_3_deg 12.063 r_long_range_B_refined 8.093 r_long_range_B_other 8.092 r_dihedral_angle_1_deg 5.759 r_scangle_other 5.28 r_scbond_it 4.034 r_scbond_other 4.031 r_mcangle_it 3.311 r_mcangle_other 3.311 r_mcbond_it 2.549 r_mcbond_other 2.547 r_angle_refined_deg 1.816 r_angle_other_deg 1.054 r_chiral_restr 0.122 r_bond_refined_d 0.017 r_gen_planes_refined 0.01 r_bond_other_d 0.004 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 3678 Nucleic Acid Atoms Solvent Atoms 463 Heterogen Atoms 84
Software Software Software Name Purpose HKL-2000 data collection MOLREP phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling