5BWM | pdb_00005bwm

The complex structure of C3cer exoenzyme and GDP bound RhoA (NADH-bound state)


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1A2B1A2B and 3BW8
experimental modelPDB 3BW81A2B and 3BW8

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP277100 mM MES (pH 6.4), 20% PEG1500
Crystal Properties
Matthews coefficientSolvent content
2.2946.38

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 50.479α = 90
b = 50.479β = 90
c = 136.671γ = 120
Symmetry
Space GroupP 32

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 2102015-05-19MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPHOTON FACTORY BEAMLINE AR-NW12A1.00Photon FactoryAR-NW12A

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
12.55099.617.44.713477
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.52.541001.814.6

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT1A2B and 3BW82.545.561278066599.540.211030.209260.210.245960.24RANDOM76.41
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]
-0.53-0.27-0.531.73
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.317
r_dihedral_angle_4_deg26.568
r_dihedral_angle_3_deg22.405
r_long_range_B_refined9.404
r_long_range_B_other9.404
r_scangle_other5.346
r_mcangle_it4.839
r_mcangle_other4.838
r_scbond_it3.419
r_scbond_other3.412
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3074
Nucleic Acid Atoms
Solvent Atoms55
Heterogen Atoms81

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing