☰ Navigation Tabs
The structure of cyclin-dependent kinase 5 (CDK5) in complex with p25 and Compound 7
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 2.71 54.69
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 117.61 α = 90 b = 117.61 β = 90 c = 154.01 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 2019-03-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-D 1.12709 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 2.91 38.67 99.9 0.169 0.173 0.039 0.998 15.5 19.9 27572
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 2.91 2.99 100 1.786 1.83 0.394 0.69 21.1
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 2.91 38.5 26146 1392 99.85 0.2539 0.2523 0.2528 0.2839 0.2842 RANDOM 89.173
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] -0.29 -0.14 -0.29 0.93
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.354 r_dihedral_angle_4_deg 18.914 r_dihedral_angle_3_deg 16.647 r_dihedral_angle_1_deg 6.592 r_angle_refined_deg 1.354 r_angle_other_deg 1.087 r_chiral_restr 0.054 r_bond_refined_d 0.005 r_gen_planes_refined 0.005 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.354 r_dihedral_angle_4_deg 18.914 r_dihedral_angle_3_deg 16.647 r_dihedral_angle_1_deg 6.592 r_angle_refined_deg 1.354 r_angle_other_deg 1.087 r_chiral_restr 0.054 r_bond_refined_d 0.005 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6865 Nucleic Acid Atoms Solvent Atoms 7 Heterogen Atoms 74
Software Software Software Name Purpose Aimless data scaling REFMAC refinement PDB_EXTRACT data extraction XDS data reduction PHASER phasing