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Dimeric structure of LRRK2 GTPase domain
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3DPU RocCOR domain (3DPU)
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 MICROBATCH 6.5 298 100mM KSCN, 25% PEGMME 2000, 0.1M BisTris pH 6.5
Crystal Properties Matthews coefficient Solvent content 2.15 42.88
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 44.647 α = 90 b = 103.688 β = 101.2 c = 44.593 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 2016-10-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 23-ID-D 1.0331 APS 23-ID-D
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 50 98.7 0.072 0.078 0.031 5.6 6.1 31247
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 1.9 1.93 91.7 0.457 0.516 0.233 0.874 4.3
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 RocCOR domain (3DPU) 1.95 43.8 27245 1458 99.1 0.1623 0.1603 0.1686 0.1962 0.1989 RANDOM 46.293
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] 8.28 7.23 -13.9 5.62
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.555 r_dihedral_angle_3_deg 16.806 r_dihedral_angle_4_deg 12.935 r_dihedral_angle_1_deg 6.921 r_angle_refined_deg 1.366 r_angle_other_deg 1.2 r_rigid_bond_restr 1.127 r_chiral_restr 0.052 r_bond_refined_d 0.004 r_gen_planes_refined 0.004
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.555 r_dihedral_angle_3_deg 16.806 r_dihedral_angle_4_deg 12.935 r_dihedral_angle_1_deg 6.921 r_angle_refined_deg 1.366 r_angle_other_deg 1.2 r_rigid_bond_restr 1.127 r_chiral_restr 0.052 r_bond_refined_d 0.004 r_gen_planes_refined 0.004 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2893 Nucleic Acid Atoms Solvent Atoms 249 Heterogen Atoms 60
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHASER phasing PDB_EXTRACT data extraction