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Crystal structure of MAP2K7 complexed with a covalent inhibitor 12
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5Y90
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 277 PEG3350
Crystal Properties Matthews coefficient Solvent content 2.46 50
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 60.965 α = 90 b = 70.517 β = 90 c = 84.346 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 95 PIXEL DECTRIS EIGER X 16M 2019-03-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-17A 0.98 Photon Factory BL-17A
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 2.06 50 99.8 0.062 17.4 6.5 23058
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 2.06 2.19 0.47
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 5y90 2.061 46.162 23058 1245 99.801 0.184 0.1816 0.1903 0.2236 0.227 40.38
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] 1.176 -1.318 0.142
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.19 r_dihedral_angle_4_deg 24.242 r_dihedral_angle_3_deg 16.02 r_lrange_it 10.343 r_lrange_other 10.342 r_scangle_it 7.769 r_scangle_other 7.767 r_dihedral_angle_1_deg 6.948 r_mcangle_it 5.646 r_mcangle_other 5.645
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.19 r_dihedral_angle_4_deg 24.242 r_dihedral_angle_3_deg 16.02 r_lrange_it 10.343 r_lrange_other 10.342 r_scangle_it 7.769 r_scangle_other 7.767 r_dihedral_angle_1_deg 6.948 r_mcangle_it 5.646 r_mcangle_other 5.645 r_scbond_it 5.195 r_scbond_other 5.195 r_mcbond_it 3.857 r_mcbond_other 3.856 r_angle_refined_deg 1.696 r_angle_other_deg 1.36 r_symmetry_nbd_refined 0.259 r_nbd_refined 0.226 r_nbd_other 0.192 r_symmetry_nbd_other 0.19 r_xyhbond_nbd_refined 0.182 r_nbtor_refined 0.169 r_symmetry_xyhbond_nbd_refined 0.146 r_symmetry_nbtor_other 0.083 r_chiral_restr 0.08 r_symmetry_xyhbond_nbd_other 0.036 r_bond_refined_d 0.011 r_gen_planes_refined 0.009 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2244 Nucleic Acid Atoms Solvent Atoms 104 Heterogen Atoms 32
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling MOLREP phasing