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LRRK2 Roc domain RP (Ras-pocket) complexed to Divarasib
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6XAF
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 277 Morpheus Fusion C7:
30 mM Halides
0.12 M Monosaccharide 1
0.1 M Buffer System 1 pH 6.5
30% Precipitant mix 1
Crystal Properties Matthews coefficient Solvent content 2.41 48.9
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 40.411 α = 90 b = 98.379 β = 90 c = 105.203 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 PILATUS3 6M 2023-10-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 2.0.1 1.02808 ALS 2.0.1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.3 49.19 99.8 0.332 0.129 0.978 9.9 6.2 19323
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 2.3 2.38 99.7 0.715 2.4 6.4
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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2.3 35.22 19267 1935 99.62 0.231 0.2268 0.2276 0.2668 0.2654 53.74
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 17.1388 f_angle_d 0.8097 f_chiral_restr 0.0495 f_plane_restr 0.0089 f_bond_d 0.0051
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2644 Nucleic Acid Atoms Solvent Atoms 96 Heterogen Atoms 149
Software Software Software Name Purpose PHENIX refinement XDS data reduction XDS data scaling PHENIX phasing