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The Crystal Structure of MNK2 from Biortus.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2AC3
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 0.2M NH4Ac, 0.1M Bis-Tris pH5.5, 25% PEG 3350
Crystal Properties Matthews coefficient Solvent content 3.21 61.71
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 103.859 α = 90 b = 103.859 β = 90 c = 73.29 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 2021-10-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL45XU 1 SPring-8 BL45XU
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 2.6 45.013 100 0.081 27.5 14.6 14349
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 2.6 2.72 0.87 3.5
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 2.6 45.013 14349 645 99.951 0.193 0.1901 0.1979 0.2536 0.2595 62.713
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] -1.031 -0.516 -1.031 3.346
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 14.536 r_dihedral_angle_3_deg 12.909 r_lrange_other 11.349 r_lrange_it 11.348 r_scangle_it 7.843 r_scangle_other 7.841 r_mcangle_it 7.743 r_mcangle_other 7.74 r_dihedral_angle_1_deg 6.201 r_dihedral_angle_2_deg 5.631
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 14.536 r_dihedral_angle_3_deg 12.909 r_lrange_other 11.349 r_lrange_it 11.348 r_scangle_it 7.843 r_scangle_other 7.841 r_mcangle_it 7.743 r_mcangle_other 7.74 r_dihedral_angle_1_deg 6.201 r_dihedral_angle_2_deg 5.631 r_scbond_it 4.865 r_scbond_other 4.864 r_mcbond_it 4.775 r_mcbond_other 4.764 r_dihedral_angle_other_3_deg 4.687 r_angle_refined_deg 1.226 r_angle_other_deg 0.415 r_symmetry_xyhbond_nbd_refined 0.267 r_nbd_refined 0.204 r_symmetry_nbd_refined 0.194 r_symmetry_nbd_other 0.189 r_nbd_other 0.185 r_nbtor_refined 0.179 r_xyhbond_nbd_refined 0.154 r_symmetry_nbtor_other 0.076 r_symmetry_xyhbond_nbd_other 0.069 r_chiral_restr 0.056 r_gen_planes_refined 0.005 r_bond_refined_d 0.004 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2199 Nucleic Acid Atoms Solvent Atoms 76 Heterogen Atoms 30
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing