7S0Y | pdb_00007s0y

Structures of TcdB in complex with Cdc42


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2BVM 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP2910.1 M sodium cacodylate (pH 6.6), 2.4 M ammonium sulfate, and 2.5% (v/v) Jeffamine M-600 (pH 7.0)
Crystal Properties
Matthews coefficientSolvent content
2.9157.67

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 122.354α = 90
b = 140.948β = 90
c = 111.803γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 16M2018-07-12MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 24-ID-C0.97918APS24-ID-C

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)CC (Half)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
12.79111.81000.0630.99916.96.724433
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.792.940.8652.9

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 REPLACEMENTTHROUGHOUT2BVM2.7992.423173124199.930.216660.214370.220.259240.26RANDOM77.173
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]
-1.824.68-2.86
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.721
r_dihedral_angle_4_deg15.1
r_dihedral_angle_3_deg14.801
r_long_range_B_other9.517
r_long_range_B_refined9.514
r_mcangle_other6.996
r_mcangle_it6.994
r_scangle_other6.46
r_dihedral_angle_1_deg6.35
r_mcbond_it4.524
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.721
r_dihedral_angle_4_deg15.1
r_dihedral_angle_3_deg14.801
r_long_range_B_other9.517
r_long_range_B_refined9.514
r_mcangle_other6.996
r_mcangle_it6.994
r_scangle_other6.46
r_dihedral_angle_1_deg6.35
r_mcbond_it4.524
r_mcbond_other4.512
r_scbond_it4.198
r_scbond_other4.124
r_angle_refined_deg1.31
r_angle_other_deg1.159
r_chiral_restr0.051
r_bond_refined_d0.004
r_gen_planes_refined0.004
r_bond_other_d0.001
r_gen_planes_other0.001
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 Atoms5787
Nucleic Acid Atoms
Solvent Atoms23
Heterogen Atoms110

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
PHENIXphasing