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Crystal Structure of Human DAPK1 Catalytic Subunit Complexed with Compound MW01-30-035SRM
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1JKS
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 295 2M LiSO4, 5mM MW01-30-035SRM
Crystal Properties Matthews coefficient Solvent content 1.92 35.88
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 46.931 α = 90 b = 62.407 β = 90 c = 88.368 γ = 90
Symmetry Space Group P 21 21 21
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 Bimorph KB Mirrors 2022-10-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-D 1.12704 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 1.49 50.98 99.5 0.087 0.093 0.034 0.998 11.6 7.4 42907
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 1.49 1.57 98.7 1.238 1.327 0.472 0.735 7.6
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Cut-off Sigma (F) 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 1.49 31.2 1.35 42841 2207 99.27 0.1713 0.1702 0.182 0.1909 0.2015 Random
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 5.427 f_angle_d 0.959 f_chiral_restr 0.077 f_plane_restr 0.01 f_bond_d 0.009
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2255 Nucleic Acid Atoms Solvent Atoms 210 Heterogen Atoms 25
Software Software Software Name Purpose PHENIX refinement REFMAC phasing Aimless data scaling PDB_EXTRACT data extraction autoPROC data reduction