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The structure of cyclin-dependent kinase 5 (CDK5) in complex with p25 and Compound 1
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 2.77 55.66
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 118.37 α = 90 b = 118.37 β = 90 c = 155.37 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 2018-08-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-D 1.07809 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 2.09 51.79 100 0.078 0.081 0.018 1 24.9 20 74979
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 2.09 2.14 100 1.423 1.464 0.339 0.782 18.4
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 2.09 51.79 71280 3645 99.95 0.2022 0.2009 0.2069 0.2287 0.2296 RANDOM 63.908
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] -0.17 -0.09 -0.17 0.56
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.166 r_dihedral_angle_4_deg 18.056 r_dihedral_angle_3_deg 14.609 r_dihedral_angle_1_deg 6.546 r_angle_refined_deg 1.356 r_angle_other_deg 1.209 r_chiral_restr 0.066 r_bond_refined_d 0.007 r_gen_planes_refined 0.006 r_bond_other_d 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.166 r_dihedral_angle_4_deg 18.056 r_dihedral_angle_3_deg 14.609 r_dihedral_angle_1_deg 6.546 r_angle_refined_deg 1.356 r_angle_other_deg 1.209 r_chiral_restr 0.066 r_bond_refined_d 0.007 r_gen_planes_refined 0.006 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6820 Nucleic Acid Atoms Solvent Atoms 372 Heterogen Atoms 131
Software Software Software Name Purpose Aimless data scaling REFMAC refinement PDB_EXTRACT data extraction XDS data reduction PHASER phasing