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Crystal structure of LIMK1 mutant D460N bound to small molecule inhibitor cLIMK1i
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5HVJ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 289.15 Morpheus condition A8 consisted of 0.06 M divalents, 0.1 M Buffer System 2, pH 7.5, and 37.5% (v/v) Precipitant Mix 4. Morpheus condition D12 consisted of 0.12 M alcohols, 0.1 M Buffer System 3, pH 8.5, and 37.5% Precipitant Mix 4.
Crystal Properties Matthews coefficient Solvent content 2.21 44.4
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 54.216 α = 90 b = 59.52 β = 102.038 c = 101.654 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 PILATUS3 6M 2024-02-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON CLSI BEAMLINE 08B1-1 1.18061 CLSI 08B1-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 1.94 51.45 67.6 0.99 18.5 6.3 32077 36.93
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.94 2 0.71 1.5
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 1.94 51.07 1.35 32077 1592 67.58 0.1833 0.181 0.1813 0.2279 0.2276 49.72
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 16.4462 f_angle_d 1.0112 f_chiral_restr 0.0592 f_plane_restr 0.0086 f_bond_d 0.0081
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4390 Nucleic Acid Atoms Solvent Atoms 186 Heterogen Atoms 58
Software Software Software Name Purpose PHENIX refinement autoPROC data reduction autoPROC data scaling PHENIX phasing