☰ Navigation Tabs
The Crystal Structure of MAPK13 from Biortus.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4YNO
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 50mM (NH4)2 tartrate, 18% PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.43 49.29
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 61.402 α = 90 b = 69.113 β = 90 c = 92.83 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 EIGER X 9M 2023-07-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON CLSI BEAMLINE 08ID-1 0.95371 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 1.5 38.56 98.2 0.072 20 13.8 62675
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 1.5 1.54 0.833
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 1.5 38.56 62624 3164 97.976 0.126 0.1239 0.1184 0.171 0.1667 21.967
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] -1.208 2.912 -1.703
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 14.994 r_dihedral_angle_3_deg 13.536 r_dihedral_angle_2_deg 6.678 r_dihedral_angle_1_deg 5.778 r_rigid_bond_restr 5.569 r_lrange_it 5.338 r_lrange_other 4.668 r_scangle_it 4.614 r_scangle_other 4.613 r_scbond_it 3.874
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 14.994 r_dihedral_angle_3_deg 13.536 r_dihedral_angle_2_deg 6.678 r_dihedral_angle_1_deg 5.778 r_rigid_bond_restr 5.569 r_lrange_it 5.338 r_lrange_other 4.668 r_scangle_it 4.614 r_scangle_other 4.613 r_scbond_it 3.874 r_scbond_other 3.874 r_mcangle_other 3.748 r_mcangle_it 3.743 r_mcbond_it 3.495 r_mcbond_other 3.492 r_angle_refined_deg 1.437 r_angle_other_deg 0.52 r_symmetry_xyhbond_nbd_refined 0.222 r_nbd_refined 0.216 r_symmetry_nbd_refined 0.199 r_nbd_other 0.195 r_symmetry_nbd_other 0.188 r_xyhbond_nbd_refined 0.187 r_nbtor_refined 0.185 r_chiral_restr 0.084 r_symmetry_nbtor_other 0.078 r_bond_refined_d 0.009 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2803 Nucleic Acid Atoms Solvent Atoms 498 Heterogen Atoms 24
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing