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The Crystal Structure of N-terminal kinase domain of human RSK-1 from Biortus.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2Z7Q
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 0.1M MgAC2, 0.1M Nacacodylate pH6.5, 15% PEG 6000
Crystal Properties Matthews coefficient Solvent content 2.89 57.49
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 33.911 α = 90 b = 54.346 β = 94.075 c = 207.028 γ = 90
Symmetry Space Group I 1 2 1
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 2021-11-12 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 2.55 33.7 93.8 0.069 6 2.9 11642
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 2.55 2.66 0.456
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 33.7 11641 606 93.502 0.206 0.2032 0.2088 0.2517 0.2531 64.192
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] -5.626 -0.381 9.58 -3.86
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 18.635 r_dihedral_angle_6_deg 16.259 r_lrange_other 12.744 r_lrange_it 12.743 r_scangle_it 9.761 r_scangle_other 9.759 r_mcangle_other 9.245 r_mcangle_it 9.24 r_dihedral_angle_2_deg 8.326 r_dihedral_angle_1_deg 8.313
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 18.635 r_dihedral_angle_6_deg 16.259 r_lrange_other 12.744 r_lrange_it 12.743 r_scangle_it 9.761 r_scangle_other 9.759 r_mcangle_other 9.245 r_mcangle_it 9.24 r_dihedral_angle_2_deg 8.326 r_dihedral_angle_1_deg 8.313 r_scbond_it 6.507 r_scbond_other 6.504 r_mcbond_it 6.024 r_mcbond_other 5.993 r_angle_refined_deg 1.572 r_angle_other_deg 0.496 r_nbd_refined 0.233 r_xyhbond_nbd_refined 0.224 r_symmetry_nbd_other 0.201 r_nbtor_refined 0.183 r_nbd_other 0.18 r_symmetry_xyhbond_nbd_refined 0.175 r_symmetry_nbd_refined 0.161 r_symmetry_nbtor_other 0.083 r_chiral_restr_other 0.081 r_chiral_restr 0.066 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 2113 Nucleic Acid Atoms Solvent Atoms 51 Heterogen Atoms 43
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing