2A9K

Crystal structure of the C3bot-NAD-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 DROP72930.2 M ammonium citrate pH 7.0, 25% PEG 3350, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.448

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 35.26α = 90
b = 113.85β = 106.4
c = 56.31γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATEMARRESEARCHOSMIC BLUE2004-09-30MSINGLE 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
11.732090.20.04913.22.94007840078-3
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)
11.731.8362.60.2393.6

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, 1UAD1.7319.03400773807320041000.188340.188340.186480.22465RANDOM21.023
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]
-0.790.42-0.421.45
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.09
r_dihedral_angle_4_deg16.503
r_dihedral_angle_3_deg13.677
r_dihedral_angle_1_deg5.202
r_scangle_it2.08
r_scbond_it1.291
r_angle_refined_deg1.11
r_mcangle_it0.816
r_mcbond_it0.485
r_nbtor_refined0.301
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.09
r_dihedral_angle_4_deg16.503
r_dihedral_angle_3_deg13.677
r_dihedral_angle_1_deg5.202
r_scangle_it2.08
r_scbond_it1.291
r_angle_refined_deg1.11
r_mcangle_it0.816
r_mcbond_it0.485
r_nbtor_refined0.301
r_symmetry_vdw_refined0.235
r_nbd_refined0.191
r_xyhbond_nbd_refined0.186
r_symmetry_hbond_refined0.105
r_chiral_restr0.077
r_bond_refined_d0.008
r_gen_planes_refined0.003
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2995
Nucleic Acid Atoms
Solvent Atoms210
Heterogen Atoms73

Software

Software
Software NamePurpose
MAR345data collection
XDSdata reduction
MOLREPphasing
REFMACrefinement
XDSdata scaling