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Legionella effector AnkX in complex with human Rab1b
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4BES 4BES, 3NKV experimental model PDB 3NKV 4BES, 3NKV
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 293 3.5 M Sodium formate
Crystal Properties Matthews coefficient Solvent content 3.72 66.92
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 171.35 α = 90 b = 68.47 β = 98.93 c = 137.37 γ = 90
Symmetry Space Group C 1 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 EIGER X 16M 2018-10-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06SA 1.0 SLS X06SA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 3.2 50 97.5 0.045 0.999 13.9 3.1 25684
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3.2 3.3 0.57 0.813 2.3
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 4BES, 3NKV 3.2 30 24372 1283 97.43 0.2493 0.2471 0.249 0.2879 0.29 RANDOM 138.743
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] -3.24 -3.23 13.21 -8.53
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.21 r_dihedral_angle_3_deg 16.364 r_dihedral_angle_4_deg 12.102 r_dihedral_angle_1_deg 5.692 r_angle_refined_deg 1.236 r_angle_other_deg 1.029 r_rigid_bond_restr 0.154 r_chiral_restr 0.042 r_bond_refined_d 0.002 r_gen_planes_refined 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.21 r_dihedral_angle_3_deg 16.364 r_dihedral_angle_4_deg 12.102 r_dihedral_angle_1_deg 5.692 r_angle_refined_deg 1.236 r_angle_other_deg 1.029 r_rigid_bond_restr 0.154 r_chiral_restr 0.042 r_bond_refined_d 0.002 r_gen_planes_refined 0.002 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7528 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 29
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction XDS data reduction XSCALE data scaling PHASER phasing