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LIM Domain Kinase 2 (LIMK2) bound to compound 52
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7QHG
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.4 293 16% PEG8000
0.04M potassium phosphate dibasic
20% glycerol
Crystal Properties Matthews coefficient Solvent content 3.07 59.93
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 86.911 α = 90 b = 86.921 β = 94.38 c = 103.297 γ = 90
Symmetry Space Group P 1 21 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 16M 2021-09-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06SA 1.00002 SLS X06SA
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 2.59 45.83 99.5 0.082 8.25 3.3 47823 42.58
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 2.59 2.68 0.556 3.4
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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2.59 45.83 1.34 47717 2380 99.52 0.2413 0.2388 0.2384 0.2875 0.2868 54.77
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 5.5591 f_angle_d 0.8208 f_chiral_restr 0.0497 f_plane_restr 0.0068 f_bond_d 0.0057
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8006 Nucleic Acid Atoms Solvent Atoms 13 Heterogen Atoms 140
Software Software Software Name Purpose MOSFLM data reduction Aimless data scaling PHASER phasing Coot model building PHENIX refinement