4XSG

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


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP277100 mM MES (pH 6.4), 20% PEG1500
Crystal Properties
Matthews coefficientSolvent content
2.1542.7

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 50.745α = 90
b = 50.745β = 90
c = 135.871γ = 120
Symmetry
Space GroupP 32

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315r2014-11-01MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPHOTON FACTORY BEAMLINE BL-5A1Photon FactoryBL-5A

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
11.85010039.35.736314

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-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT1A2B, 3BW81.845.2934457180899.950.177140.174830.22274RANDOM40.646
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]
-0.05-0.03-0.050.16
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.387
r_dihedral_angle_4_deg16.142
r_dihedral_angle_3_deg12.856
r_long_range_B_refined7.766
r_long_range_B_other7.766
r_scangle_other6.117
r_dihedral_angle_1_deg5.957
r_scbond_it4.137
r_scbond_other4.137
r_mcangle_it4.113
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.387
r_dihedral_angle_4_deg16.142
r_dihedral_angle_3_deg12.856
r_long_range_B_refined7.766
r_long_range_B_other7.766
r_scangle_other6.117
r_dihedral_angle_1_deg5.957
r_scbond_it4.137
r_scbond_other4.137
r_mcangle_it4.113
r_mcangle_other4.113
r_mcbond_it3.083
r_mcbond_other3.073
r_angle_refined_deg1.35
r_angle_other_deg0.918
r_chiral_restr0.085
r_bond_refined_d0.009
r_gen_planes_refined0.006
r_bond_other_d0.002
r_gen_planes_other0.002
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3069
Nucleic Acid Atoms
Solvent Atoms308
Heterogen Atoms41

Software

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