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Crystal structure of the C3bot-RalA complex reveals a novel type of action of a bacterial exoenzyme
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1G24 1G24, 1UAD experimental model PDB 1UAD 1G24, 1UAD
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.5 293 0.2 M ammonium sulfate, 0.1 M bis-Tris, 25% w/v polyethylene glycol 3350, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.4 48
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 34.94 α = 90 b = 112.83 β = 105.1 c = 56.35 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 IMAGE PLATE MARRESEARCH Osmic Blue 2004-07-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RU300 1.5418
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym I (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 1.8 20 91.8 0.059 11.8 2.3 39025 35816 -3 22.3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.8 1.91 62.9 0.345 2.3 1.6 3978
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) 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 1G24, 1UAD 1.81 19.57 35815 34024 1791 100 0.182 0.182 0.18 0.181 0.217 0.2185 RANDOM 17.49
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] -0.56 0.46 0.09 0.7
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.533 r_dihedral_angle_4_deg 15.084 r_dihedral_angle_3_deg 13.995 r_dihedral_angle_1_deg 5.769 r_scangle_it 2.257 r_scbond_it 1.398 r_angle_refined_deg 1.048 r_mcangle_it 0.886 r_mcbond_it 0.499 r_nbtor_refined 0.305
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.533 r_dihedral_angle_4_deg 15.084 r_dihedral_angle_3_deg 13.995 r_dihedral_angle_1_deg 5.769 r_scangle_it 2.257 r_scbond_it 1.398 r_angle_refined_deg 1.048 r_mcangle_it 0.886 r_mcbond_it 0.499 r_nbtor_refined 0.305 r_symmetry_vdw_refined 0.207 r_nbd_refined 0.193 r_xyhbond_nbd_refined 0.123 r_symmetry_hbond_refined 0.106 r_chiral_restr 0.073 r_metal_ion_refined 0.016 r_bond_refined_d 0.007 r_gen_planes_refined 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2995 Nucleic Acid Atoms Solvent Atoms 330 Heterogen Atoms 29
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction MAR345 data collection XDS data scaling MOLREP phasing