4XSH

The complex structure of C3cer exoenzyme and GTP 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
2.2846.08

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 50.424α = 90
b = 50.424β = 90
c = 136.667γ = 120
Symmetry
Space GroupP 32

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS VII2014-09-30MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU MICROMAX-007 HF1.54

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
12.35099.9215.513464

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 and 3BW82.545.5612085133499.760.195890.18950.25353RANDOM68.204
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]
0.180.090.18-0.58
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.035
r_dihedral_angle_4_deg23.329
r_dihedral_angle_3_deg20.005
r_long_range_B_refined8.909
r_long_range_B_other8.909
r_scangle_other5.74
r_dihedral_angle_1_deg5.267
r_mcangle_it4.546
r_mcangle_other4.545
r_scbond_it3.639
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.035
r_dihedral_angle_4_deg23.329
r_dihedral_angle_3_deg20.005
r_long_range_B_refined8.909
r_long_range_B_other8.909
r_scangle_other5.74
r_dihedral_angle_1_deg5.267
r_mcangle_it4.546
r_mcangle_other4.545
r_scbond_it3.639
r_scbond_other3.639
r_mcbond_it2.985
r_mcbond_other2.983
r_angle_refined_deg1.259
r_angle_other_deg1.098
r_chiral_restr0.051
r_bond_refined_d0.011
r_gen_planes_refined0.006
r_bond_other_d0.003
r_gen_planes_other0.003
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 Atoms3074
Nucleic Acid Atoms
Solvent Atoms55
Heterogen Atoms89

Software

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