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Structure of DrrA from Legionella pneumophilia in complex with human Rab8a
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3NKU 3NKU, 4LHV experimental model PDB 4LHV 3NKU, 4LHV
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 9 293 0.1M bicine, pH 9, 2.4M ammonium sulphate
Crystal Properties Matthews coefficient Solvent content 3.8 45
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 142.309 α = 90 b = 142.309 β = 90 c = 76.616 γ = 120
Symmetry Space Group P 3 2 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 2M 2018-09-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE MASSIF-1 0.966 ESRF MASSIF-1
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 2.14 48.06 99.7 0.2 0.206 0.045 0.99 15.57 20 49091 43.52
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 2.14 2.22 96.97 2.43 2.5 0.57 0.43 0.93 18.3
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 3NKU, 4LHV 2.14 48.06 46650 2441 99.63 0.2084 0.2068 0.2173 0.2385 0.2416 RANDOM 50.306
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] -0.07 -0.03 -0.07 0.22
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.087 r_dihedral_angle_4_deg 16.777 r_dihedral_angle_3_deg 14.769 r_dihedral_angle_1_deg 6.091 r_angle_refined_deg 1.256 r_angle_other_deg 1.148 r_chiral_restr 0.05 r_bond_refined_d 0.004 r_gen_planes_refined 0.004 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.087 r_dihedral_angle_4_deg 16.777 r_dihedral_angle_3_deg 14.769 r_dihedral_angle_1_deg 6.091 r_angle_refined_deg 1.256 r_angle_other_deg 1.148 r_chiral_restr 0.05 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 4115 Nucleic Acid Atoms Solvent Atoms 113 Heterogen Atoms 116
Software Software Software Name Purpose XDS data reduction REFMAC refinement PDB_EXTRACT data extraction XDS data scaling PHASER phasing