2PAV

Ternary complex of Profilin-Actin with the Last Poly-Pro of Human VASP


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2BTFPDB ENTRY 2BTF

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.4277.15200 mM sodium formate, 20% PEG 3350, pH 7.4, VAPOR DIFFUSION, SITTING DROP, temperature 277.15K
Crystal Properties
Matthews coefficientSolvent content
2.1943.94

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 37.467α = 90
b = 75.46β = 90
c = 180.741γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray200CCDADSC QUANTUM 3152005-12-19MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 14-BM-C0.90020APS14-BM-C

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (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
11.85098.10.0760.07628.17479474794715
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.81.8697.70.3450.3455.75.94691

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 2BTF1.847.094533847739240198.140.160.160.1580.208RANDOM15.002
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]
0.09-0.1
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.532
r_dihedral_angle_4_deg14.34
r_dihedral_angle_3_deg14.169
r_dihedral_angle_1_deg5.92
r_scangle_it4.09
r_scbond_it2.73
r_angle_refined_deg1.663
r_mcangle_it1.61
r_mcbond_it1.096
r_nbtor_refined0.312
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.532
r_dihedral_angle_4_deg14.34
r_dihedral_angle_3_deg14.169
r_dihedral_angle_1_deg5.92
r_scangle_it4.09
r_scbond_it2.73
r_angle_refined_deg1.663
r_mcangle_it1.61
r_mcbond_it1.096
r_nbtor_refined0.312
r_symmetry_vdw_refined0.248
r_nbd_refined0.21
r_symmetry_hbond_refined0.204
r_xyhbond_nbd_refined0.197
r_chiral_restr0.187
r_metal_ion_refined0.036
r_bond_refined_d0.019
r_gen_planes_refined0.008
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3968
Nucleic Acid Atoms
Solvent Atoms542
Heterogen Atoms32

Software

Software
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
SCALEPACKdata scaling
AMoREphasing