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The structure of cyclin-dependent kinase 5 (CDK5) in complex with p25 and Compound 24
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3O0G
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.5 291 0.1M MES pH 5.5, 0.3M MgCl2, 20% PEG3350
Crystal Properties Matthews coefficient Solvent content 2.73 54.94
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 118.06 α = 90 b = 118.06 β = 90 c = 153.69 γ = 120
Symmetry Space Group P 32 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 EIGER X 9M 2020-02-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-D 1.12713 APS 21-ID-D
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 3.05 48.51 100 0.144 0.149 0.035 0.999 14.3 18.1 24161
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3.05 3.26 100 2.565 2.636 0.605 0.565 18.6
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 3O0G 3.05 48.51 22918 1207 99.9 0.2279 0.2254 0.2242 0.2715 0.2685 RANDOM 133.419
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] -0.14 -0.07 -0.14 0.44
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.246 r_dihedral_angle_4_deg 16.62 r_dihedral_angle_3_deg 15.435 r_dihedral_angle_1_deg 6.043 r_angle_refined_deg 1.244 r_angle_other_deg 1.048 r_chiral_restr 0.047 r_bond_refined_d 0.003 r_gen_planes_refined 0.003 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.246 r_dihedral_angle_4_deg 16.62 r_dihedral_angle_3_deg 15.435 r_dihedral_angle_1_deg 6.043 r_angle_refined_deg 1.244 r_angle_other_deg 1.048 r_chiral_restr 0.047 r_bond_refined_d 0.003 r_gen_planes_refined 0.003 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6954 Nucleic Acid Atoms Solvent Atoms 69 Heterogen Atoms 183
Software Software Software Name Purpose Aimless data scaling REFMAC refinement PDB_EXTRACT data extraction XDS data reduction PHASER phasing