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LIM Domain Kinase 2 (LIMK2) In Complex With TH-300
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4TPT
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 277 0.1 M bis-tris-propane pH 7.5
0.2 M Na2SO4
10% ethylene glycol
17% PEG3.35K
Crystal Properties Matthews coefficient Solvent content 2.3 46.49
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 63.275 α = 90 b = 66.605 β = 97.43 c = 82.124 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 PILATUS 6M 2016-04-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I02 0.9795 Diamond I02
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 1.9 66.61 97.5 0.072 11.1 3.3 51845
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 1.9 1.94 99.5 0.659 2.2 3.2
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 4TPT 1.9 66.61 49231 2594 97.45 0.19666 0.19485 0.2032 0.23042 0.2343 RANDOM 28.856
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] -0.42 0.03 0.53 -0.11
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.117 r_dihedral_angle_4_deg 18.688 r_dihedral_angle_3_deg 13.476 r_dihedral_angle_1_deg 5.953 r_long_range_B_refined 5.937 r_long_range_B_other 5.936 r_scangle_other 4.697 r_mcangle_it 3.73 r_mcangle_other 3.729 r_scbond_it 3.153
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.117 r_dihedral_angle_4_deg 18.688 r_dihedral_angle_3_deg 13.476 r_dihedral_angle_1_deg 5.953 r_long_range_B_refined 5.937 r_long_range_B_other 5.936 r_scangle_other 4.697 r_mcangle_it 3.73 r_mcangle_other 3.729 r_scbond_it 3.153 r_scbond_other 3.152 r_mcbond_it 2.629 r_mcbond_other 2.628 r_angle_refined_deg 1.9 r_angle_other_deg 1.078 r_chiral_restr 0.113 r_bond_refined_d 0.018 r_gen_planes_refined 0.011 r_bond_other_d 0.002 r_gen_planes_other 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4214 Nucleic Acid Atoms Solvent Atoms 133 Heterogen Atoms 68
Software Software Software Name Purpose REFMAC refinement xia2 data reduction xia2 data scaling PHASER phasing