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The Crystal Structure of MAPK11 from Biortus
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3GP0
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 0.1M Bis-Tris pH6.5, 28% PEGMME2,000
Crystal Properties Matthews coefficient Solvent content 2.15 42.82
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 39.061 α = 90 b = 61.86 β = 90 c = 147.437 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 100 PIXEL DECTRIS PILATUS3 6M 2023-05-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON CLSI BEAMLINE 08ID-1 0.95374 CLSI 08ID-1
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 3.3 49.15 100 0.199 9.3 7.3 5815
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 3.3 3.57 0.827
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 3.301 49.15 5780 284 99.948 0.209 0.2054 0.2112 0.2781 0.2838 78.808
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] -2.978 7.254 -4.276
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 11.107 r_dihedral_angle_6_deg 10.801 r_lrange_it 6.091 r_lrange_other 6.09 r_dihedral_angle_1_deg 5.281 r_mcangle_it 3.606 r_mcangle_other 3.606 r_scangle_it 2.862 r_scangle_other 2.861 r_dihedral_angle_2_deg 2.609
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 11.107 r_dihedral_angle_6_deg 10.801 r_lrange_it 6.091 r_lrange_other 6.09 r_dihedral_angle_1_deg 5.281 r_mcangle_it 3.606 r_mcangle_other 3.606 r_scangle_it 2.862 r_scangle_other 2.861 r_dihedral_angle_2_deg 2.609 r_mcbond_it 2.049 r_mcbond_other 2.048 r_scbond_it 1.598 r_scbond_other 1.597 r_angle_refined_deg 0.685 r_angle_other_deg 0.239 r_nbd_refined 0.179 r_symmetry_nbd_other 0.169 r_nbtor_refined 0.168 r_nbd_other 0.157 r_xyhbond_nbd_refined 0.132 r_symmetry_nbd_refined 0.12 r_symmetry_xyhbond_nbd_refined 0.113 r_symmetry_nbtor_other 0.072 r_chiral_restr 0.032 r_bond_refined_d 0.002 r_gen_planes_refined 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 2632 Nucleic Acid Atoms Solvent Atoms 26 Heterogen Atoms 39
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing