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The Crystal Structure of C-terminal kinase domain of RSK2 from Biortus
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5O1S
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 0.1 M Tris pH8.5, 25%PEG3,350
Crystal Properties Matthews coefficient Solvent content 2.07 40.69
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 46.513 α = 90 b = 46.513 β = 90 c = 294.07 γ = 90
Symmetry Space Group P 41 21 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 PILATUS3 6M 2021-10-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL45XU 1.000000 SPring-8 BL45XU
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 2.65 49.01 100 0.174 12.4 14.8 10370
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 2.65 2.78 0.994
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 2.65 45.984 10281 551 99.971 0.206 0.2016 0.2089 0.2803 0.2786 51.766
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] 3.143 3.143 -6.285
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.744 r_dihedral_angle_6_deg 14.353 r_lrange_other 11.347 r_lrange_it 11.343 r_dihedral_angle_1_deg 8.082 r_mcangle_it 7.938 r_mcangle_other 7.935 r_dihedral_angle_2_deg 7.837 r_scangle_it 7.45 r_scangle_other 7.448
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.744 r_dihedral_angle_6_deg 14.353 r_lrange_other 11.347 r_lrange_it 11.343 r_dihedral_angle_1_deg 8.082 r_mcangle_it 7.938 r_mcangle_other 7.935 r_dihedral_angle_2_deg 7.837 r_scangle_it 7.45 r_scangle_other 7.448 r_mcbond_it 5.14 r_mcbond_other 5.138 r_scbond_it 4.801 r_scbond_other 4.799 r_angle_refined_deg 1.518 r_angle_other_deg 0.5 r_nbd_refined 0.225 r_symmetry_nbd_refined 0.212 r_symmetry_nbd_other 0.198 r_xyhbond_nbd_refined 0.194 r_nbtor_refined 0.18 r_nbd_other 0.174 r_symmetry_xyhbond_nbd_refined 0.123 r_symmetry_nbtor_other 0.08 r_chiral_restr 0.068 r_bond_refined_d 0.008 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 2480 Nucleic Acid Atoms Solvent Atoms 58 Heterogen Atoms 11
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing