☰ Navigation Tabs
Crystal structure of menin in complex with DS-1594b
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other in house structure
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.4 283 0.1 M Na Cacodylate HCl, pH 6.4/ 1.5 M NaOAc/ 20 mM BaCl2.
Complex crystal was prepared with soaking method.
Crystal Properties Matthews coefficient Solvent content 2.94 58.1
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 141.576 α = 90 b = 70.151 β = 91.47 c = 144.426 γ = 90
Symmetry Space Group P 1 21 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS EIGER X 4M 2021-03-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-1A 1.07 Photon Factory BL-1A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) 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 2.6 49.82 99.8 0.083 0.099 0.053 0.997 3.6 3.3 87588
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.6 2.65 98.8 1.273 1.526 0.832 0.547 3.1
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 (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 2.6 25 83083 4393 99.63 0.2147 0.212 0.2164 0.2661 0.2692 RANDOM 63.327
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] -3.98 0.51 7.72 -3.76
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.683 r_dihedral_angle_3_deg 16.042 r_dihedral_angle_4_deg 14.676 r_dihedral_angle_1_deg 6.244 r_angle_refined_deg 1.177 r_chiral_restr 0.081 r_gen_planes_refined 0.005 r_bond_refined_d 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 14717 Nucleic Acid Atoms Solvent Atoms 142 Heterogen Atoms 180
Software Software Software Name Purpose Aimless data scaling REFMAC refinement PDB_EXTRACT data extraction XDS data reduction PHASER phasing