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Crystal structure of the human LRRK2 WDR domain in complex with CACHE1193-26
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6DLO
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 291 0.1 M Tris-HCl at pH 8.5, 1 M LiCl, 14% (w/v) polyethylene glycol (PEG) 6000 and 10% galactose
Crystal Properties Matthews coefficient Solvent content 2.69 54.35
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 79.162 α = 90 b = 103.064 β = 90 c = 115.301 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 EIGER2 X 16M 2023-02-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 24-ID-E 0.97918 APS 24-ID-E
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 2.6 50 96.9 0.057 0.061 0.022 1 9.7 7.5 29052
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 2.6 2.64 97.7 0.902 0.97 0.35 0.795 7.4
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 FOURIER SYNTHESIS THROUGHOUT 2.6 47.05 29020 2412 96.7 0.202 0.199 0.2043 0.24 0.2509 RANDOM 74.28
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] 13.3604 -4.5118 -8.8486
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 18.56 t_omega_torsion 3.16 t_angle_deg 1.2 t_bond_d 0.01 t_dihedral_angle_d t_incorr_chiral_ct t_pseud_angle t_trig_c_planes t_gen_planes t_it
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 18.56 t_omega_torsion 3.16 t_angle_deg 1.2 t_bond_d 0.01 t_dihedral_angle_d t_incorr_chiral_ct t_pseud_angle t_trig_c_planes t_gen_planes t_it t_nbd t_improper_torsion t_chiral_improper_torsion t_sum_occupancies t_utility_distance t_utility_angle t_utility_torsion t_ideal_dist_contact
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4773 Nucleic Acid Atoms Solvent Atoms 44 Heterogen Atoms 52
Software Software Software Name Purpose BUSTER refinement HKL-3000 data scaling REFMAC phasing HKL-3000 data reduction