2A78

Crystal structure of the C3bot-RalA complex reveals a novel type of action of a bacterial exoenzyme


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1G241G24, 1UAD
experimental modelPDB 1UAD1G24, 1UAD

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP5.52930.2 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 coefficientSolvent content
2.448

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 34.94α = 90
b = 112.83β = 105.1
c = 56.35γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATEMARRESEARCHOsmic Blue2004-07-30MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU RU3001.5418

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym I (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
11.82091.80.05911.82.33902535816-322.3
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.81.9162.90.3452.31.63978

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT1G24, 1UAD1.8119.57358153402417911000.1820.1820.180.217RANDOM17.49
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]
-0.560.460.090.7
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.533
r_dihedral_angle_4_deg15.084
r_dihedral_angle_3_deg13.995
r_dihedral_angle_1_deg5.769
r_scangle_it2.257
r_scbond_it1.398
r_angle_refined_deg1.048
r_mcangle_it0.886
r_mcbond_it0.499
r_nbtor_refined0.305
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.533
r_dihedral_angle_4_deg15.084
r_dihedral_angle_3_deg13.995
r_dihedral_angle_1_deg5.769
r_scangle_it2.257
r_scbond_it1.398
r_angle_refined_deg1.048
r_mcangle_it0.886
r_mcbond_it0.499
r_nbtor_refined0.305
r_symmetry_vdw_refined0.207
r_nbd_refined0.193
r_xyhbond_nbd_refined0.123
r_symmetry_hbond_refined0.106
r_chiral_restr0.073
r_metal_ion_refined0.016
r_bond_refined_d0.007
r_gen_planes_refined0.003
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2995
Nucleic Acid Atoms
Solvent Atoms330
Heterogen Atoms29

Software

Software
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
MAR345data collection
XDSdata scaling
MOLREPphasing