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Structure of MNK2 in complex with inhibitor NUCC-0201049
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other Unpublished structure
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.1 298 0.02 M Magnesium Chloride, 0.1 M HEPES-NaOH pH 7.1 and 29% w/v Sodium Polyacrylate 5100
Crystal Properties Matthews coefficient Solvent content 3.24 62.06
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 106.927 α = 90 b = 106.927 β = 90 c = 69.952 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 EIGER X 16M 2020-04-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON MAX IV BEAMLINE BioMAX 0.976254 MAX IV BioMAX
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 3.16 55.82 100 0.143 0.15 0.045 0.999 15.2 20.3 8187 77.3
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 3.16 3.38 100 1.183 1.241 0.374 0.864 2.8 20.9
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 FOURIER SYNTHESIS FREE R-VALUE 3.161 35.002 8166 383 99.902 0.186 0.1831 0.1927 0.2434 0.2574 99.436
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] -3.735 -1.868 -3.735 12.117
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 13.865 r_dihedral_angle_6_deg 12.102 r_lrange_it 12.076 r_lrange_other 12.074 r_mcangle_it 7.541 r_mcangle_other 7.539 r_scangle_it 7.25 r_scangle_other 7.248 r_dihedral_angle_1_deg 5.736 r_dihedral_angle_2_deg 4.571
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 13.865 r_dihedral_angle_6_deg 12.102 r_lrange_it 12.076 r_lrange_other 12.074 r_mcangle_it 7.541 r_mcangle_other 7.539 r_scangle_it 7.25 r_scangle_other 7.248 r_dihedral_angle_1_deg 5.736 r_dihedral_angle_2_deg 4.571 r_dihedral_angle_other_3_deg 4.539 r_mcbond_it 4.474 r_mcbond_other 4.47 r_scbond_it 4.266 r_scbond_other 4.264 r_angle_refined_deg 0.768 r_angle_other_deg 0.27 r_nbd_refined 0.2 r_symmetry_nbd_other 0.176 r_nbtor_refined 0.176 r_xyhbond_nbd_refined 0.149 r_nbd_other 0.119 r_symmetry_xyhbond_nbd_refined 0.108 r_symmetry_nbd_refined 0.101 r_symmetry_xyhbond_nbd_other 0.097 r_symmetry_nbtor_other 0.076 r_chiral_restr 0.038 r_gen_planes_refined 0.003 r_bond_refined_d 0.002 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2249 Nucleic Acid Atoms Solvent Atoms 19 Heterogen Atoms 29
Software Software Software Name Purpose XDS data reduction Aimless data scaling REFMAC refinement PHASER phasing