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Crystal Structure of Mnk2-D228G in complex with Inhibitor
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6CJ5
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 300.15 20-30% (w/v) polyacrylic acid 5100, 1-5% PEG 400, and 50 mM Hepes (pH 7.5)
Crystal Properties Matthews coefficient Solvent content 3.26 62.31
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 105.787 α = 90 b = 105.787 β = 90 c = 71.942 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 CCD ADSC QUANTUM 315r 2016-09-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 5.0.1 0.987 ALS 5.0.1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 3.3 56.7 98 2 4 7289
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3.3 3.5
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 6cj5 3.32 30 6688 330 98.25 0.22544 0.223 0.2379 0.27317 0.278 RANDOM 109.41
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] -4.82 -2.41 -4.82 15.63
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.47 r_dihedral_angle_3_deg 19.726 r_dihedral_angle_4_deg 18.288 r_long_range_B_refined 15.007 r_long_range_B_other 15.004 r_scangle_other 10.176 r_mcangle_other 10.149 r_mcangle_it 10.141 r_dihedral_angle_1_deg 8.383 r_mcbond_it 6.344
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.47 r_dihedral_angle_3_deg 19.726 r_dihedral_angle_4_deg 18.288 r_long_range_B_refined 15.007 r_long_range_B_other 15.004 r_scangle_other 10.176 r_mcangle_other 10.149 r_mcangle_it 10.141 r_dihedral_angle_1_deg 8.383 r_mcbond_it 6.344 r_mcbond_other 6.243 r_scbond_it 6.068 r_scbond_other 6.068 r_angle_other_deg 2.007 r_angle_refined_deg 1.572 r_chiral_restr 0.083 r_bond_refined_d 0.01 r_gen_planes_other 0.01 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2154 Nucleic Acid Atoms Solvent Atoms 6 Heterogen Atoms 26
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHASER phasing