☰ Navigation Tabs
menin in complex with MI-136
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 2.28 46.1
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 49.013 α = 90 b = 80.178 β = 90 c = 124.887 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 225 mm CCD 2012-03-10 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 1.86 50 83.2 0.078 6.8 2.9 34967
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 1.86 1.89 85.1 0.382 2.8 1748
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 1.86 36.95 34967 1750 83.26 0.1646 0.1623 0.1741 0.2081 0.2185 RANDOM 21.441
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.511 r_dihedral_angle_4_deg 15.995 r_dihedral_angle_3_deg 12.817 r_dihedral_angle_1_deg 5.977 r_angle_other_deg 3.629 r_mcangle_it 2.716 r_mcbond_it 1.763 r_mcbond_other 1.763 r_angle_refined_deg 1.613 r_chiral_restr 0.099
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.511 r_dihedral_angle_4_deg 15.995 r_dihedral_angle_3_deg 12.817 r_dihedral_angle_1_deg 5.977 r_angle_other_deg 3.629 r_mcangle_it 2.716 r_mcbond_it 1.763 r_mcbond_other 1.763 r_angle_refined_deg 1.613 r_chiral_restr 0.099 r_bond_refined_d 0.015 r_gen_planes_other 0.015 r_gen_planes_refined 0.008 r_bond_other_d
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3630 Nucleic Acid Atoms Solvent Atoms 232 Heterogen Atoms 78
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction MOLREP phasing PDB_EXTRACT data extraction DENZO data reduction SCALEPACK data scaling