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Crystal structure of the C3bot-NAD-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 7 293 0.2 M ammonium citrate pH 7.0, 25% PEG 3350, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.4 48
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 35.26 α = 90 b = 113.85 β = 106.4 c = 56.31 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 2004-09-30 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 1.73 20 90.2 0.049 13.2 2.9 40078 40078 -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 1.73 1.83 62.6 0.239 3.6
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 1.73 19.03 40077 38073 2004 100 0.18834 0.18834 0.18648 0.187 0.22465 0.2253 RANDOM 21.023
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] -0.79 0.42 -0.42 1.45
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.09 r_dihedral_angle_4_deg 16.503 r_dihedral_angle_3_deg 13.677 r_dihedral_angle_1_deg 5.202 r_scangle_it 2.08 r_scbond_it 1.291 r_angle_refined_deg 1.11 r_mcangle_it 0.816 r_mcbond_it 0.485 r_nbtor_refined 0.301
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.09 r_dihedral_angle_4_deg 16.503 r_dihedral_angle_3_deg 13.677 r_dihedral_angle_1_deg 5.202 r_scangle_it 2.08 r_scbond_it 1.291 r_angle_refined_deg 1.11 r_mcangle_it 0.816 r_mcbond_it 0.485 r_nbtor_refined 0.301 r_symmetry_vdw_refined 0.235 r_nbd_refined 0.191 r_xyhbond_nbd_refined 0.186 r_symmetry_hbond_refined 0.105 r_chiral_restr 0.077 r_bond_refined_d 0.008 r_gen_planes_refined 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2995 Nucleic Acid Atoms Solvent Atoms 210 Heterogen Atoms 73
Software Software Software Name Purpose MAR345 data collection XDS data reduction MOLREP phasing REFMAC refinement XDS data scaling