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Crystal Structure of Mnk2-D228G in complex with Tinodasertib
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2HW7
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8 292 24% (w/v) polyacrylic acid 5100, 2% (v/v) 2-Methyl-2,4-pentanediol, 100mM HEPES, pH 8.0
Crystal Properties Matthews coefficient Solvent content 3.79 67.59
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 105.91 α = 90 b = 105.91 β = 90 c = 71.5 γ = 120
Symmetry Space Group P 32 2 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 PILATUS 6M 2019-01-31 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.9763 Diamond I03
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Rrim 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 2.59 56.39 99.9 0.05 1 24.4 9.6 14740
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.59 2.66 100 1.617 0.558 1.2 8.1
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2.59 50.005 14721 738 99.932 0.211 0.2081 0.2132 0.2636 0.2598 88.708
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] 0.11 0.055 0.11 -0.357
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 16.464 r_dihedral_angle_6_deg 15.095 r_dihedral_angle_other_3_deg 11.264 r_lrange_it 9.667 r_lrange_other 9.665 r_scangle_it 8.579 r_scangle_other 8.576 r_dihedral_angle_1_deg 7.074 r_dihedral_angle_2_deg 6.976 r_mcangle_it 6.728
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 16.464 r_dihedral_angle_6_deg 15.095 r_dihedral_angle_other_3_deg 11.264 r_lrange_it 9.667 r_lrange_other 9.665 r_scangle_it 8.579 r_scangle_other 8.576 r_dihedral_angle_1_deg 7.074 r_dihedral_angle_2_deg 6.976 r_mcangle_it 6.728 r_mcangle_other 6.725 r_scbond_it 6.245 r_scbond_other 6.242 r_mcbond_it 4.709 r_mcbond_other 4.707 r_angle_refined_deg 1.358 r_chiral_restr_other 1.188 r_angle_other_deg 0.542 r_symmetry_nbd_refined 0.251 r_nbd_refined 0.228 r_symmetry_nbd_other 0.193 r_nbd_other 0.188 r_nbtor_refined 0.185 r_symmetry_xyhbond_nbd_refined 0.161 r_xyhbond_nbd_refined 0.124 r_symmetry_nbtor_other 0.083 r_chiral_restr 0.065 r_bond_refined_d 0.007 r_gen_planes_refined 0.006 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2015 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 32
Software Software Software Name Purpose REFMAC refinement xia2 data reduction Aimless data scaling PHASER phasing