2DFK

Crystal structure of the CDC42-Collybistin II complex


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1FOEPDB ENTRY 1FOE

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP8PEG 8000, Potassium dihydrogen phosphate, NaCl, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298K, pH 8.00
Crystal Properties
Matthews coefficientSolvent content
2.652

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 57.957α = 90
b = 147.499β = 90
c = 167.22γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 42003-08-30MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSLS BEAMLINE X26CNSLSX26C

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
12.155096.10.07522.54.772590239.2
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)
12.152.2383.30.5223.4

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 REPLACEMENTTHROUGHOUTPDB ENTRY 1FOE2.1547.6772076378298.20.1830.180.229RANDOM25.25
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]
-0.10.44-0.34
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg6.631
r_scangle_it5.52
r_scbond_it3.326
r_mcangle_it2.049
r_angle_refined_deg1.833
r_mcbond_it1.07
r_angle_other_deg0.981
r_symmetry_vdw_refined0.278
r_symmetry_vdw_other0.275
r_nbd_other0.24
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg6.631
r_scangle_it5.52
r_scbond_it3.326
r_mcangle_it2.049
r_angle_refined_deg1.833
r_mcbond_it1.07
r_angle_other_deg0.981
r_symmetry_vdw_refined0.278
r_symmetry_vdw_other0.275
r_nbd_other0.24
r_nbd_refined0.231
r_xyhbond_nbd_refined0.212
r_symmetry_hbond_refined0.137
r_chiral_restr0.123
r_nbtor_other0.09
r_bond_refined_d0.022
r_gen_planes_other0.012
r_gen_planes_refined0.01
r_bond_other_d0.003
r_dihedral_angle_2_deg
r_dihedral_angle_3_deg
r_dihedral_angle_4_deg
r_nbtor_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms9002
Nucleic Acid Atoms
Solvent Atoms581
Heterogen Atoms46

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMACrefinement