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Structural Basis for PI(4)P-Specific Membrane Recruitment of the Legionella pneumophila Effector DrrA/SidM
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3L0M PDB ENTRY 3L0M
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 291 4-6% PEG 3350, 100 mM Tris, 0.5 M NaCl, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 2.96 58.48
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 128.552 α = 90 b = 128.552 β = 90 c = 53.222 γ = 90
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD ADSC QUANTUM 4r 2010-09-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X12B 1.00000 NSLS X12B
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 1.83 50 99.5 38272 -3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.83 1.86 92.8
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (I) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 PDB ENTRY 3L0M 1.83 26.9 -3 38240 1906 99.75 0.1896 0.1896 0.1886 0.198 0.2079 0.221 RANDOM 27.0265
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] 0.09 0.09 -0.18
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.41 r_dihedral_angle_4_deg 17.709 r_dihedral_angle_3_deg 13.085 r_dihedral_angle_1_deg 4.922 r_mcangle_it 2.273 r_mcbond_it 1.502 r_mcbond_other 1.498 r_angle_refined_deg 1.22 r_angle_other_deg 0.735 r_chiral_restr 0.068
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.41 r_dihedral_angle_4_deg 17.709 r_dihedral_angle_3_deg 13.085 r_dihedral_angle_1_deg 4.922 r_mcangle_it 2.273 r_mcbond_it 1.502 r_mcbond_other 1.498 r_angle_refined_deg 1.22 r_angle_other_deg 0.735 r_chiral_restr 0.068 r_bond_refined_d 0.009 r_bond_other_d 0.005 r_gen_planes_refined 0.005 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2455 Nucleic Acid Atoms Solvent Atoms 195 Heterogen Atoms 36
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data collection DENZO data reduction SCALEPACK data scaling PHENIX phasing