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The Crystal Structure of MAPKAP kinase 2 domain from Biortus
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3M42
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 1.1M Sodium malonate dibasic monohydrate, 0.1M HEPES pH 7, 0.5% v/v Jeffamine ED2003
Crystal Properties Matthews coefficient Solvent content 3.73 67.01
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 103.239 α = 90 b = 103.239 β = 90 c = 166.788 γ = 120
Symmetry Space Group P 63 2 2
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 2023-09-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON AUSTRALIAN SYNCHROTRON BEAMLINE MX2 0.953732 Australian Synchrotron MX2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 2.55 49.31 100 0.998 18.2 21.5 17831
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.55 2.66 0.9 4.7
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 2.55 49.31 17799 862 100 0.17 0.1661 0.173 0.2454 0.2533 35.866
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] -0.464 -0.232 -0.464 1.504
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 16.472 r_dihedral_angle_6_deg 15.801 r_lrange_it 10.091 r_lrange_other 10.072 r_dihedral_angle_1_deg 7.368 r_scangle_it 7.349 r_scangle_other 7.347 r_mcangle_it 6.209 r_mcangle_other 6.209 r_dihedral_angle_2_deg 6.191
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 16.472 r_dihedral_angle_6_deg 15.801 r_lrange_it 10.091 r_lrange_other 10.072 r_dihedral_angle_1_deg 7.368 r_scangle_it 7.349 r_scangle_other 7.347 r_mcangle_it 6.209 r_mcangle_other 6.209 r_dihedral_angle_2_deg 6.191 r_scbond_it 4.504 r_scbond_other 4.502 r_mcbond_it 3.976 r_mcbond_other 3.966 r_angle_refined_deg 1.622 r_angle_other_deg 0.532 r_nbd_other 0.25 r_nbd_refined 0.218 r_symmetry_nbd_other 0.196 r_nbtor_refined 0.18 r_xyhbond_nbd_refined 0.177 r_symmetry_xyhbond_nbd_refined 0.133 r_symmetry_nbd_refined 0.116 r_symmetry_nbtor_other 0.084 r_chiral_restr 0.073 r_bond_refined_d 0.008 r_gen_planes_refined 0.007 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2383 Nucleic Acid Atoms Solvent Atoms 207 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing