2PBD

Ternary complex of profilin-actin with the poly-PRO-GAB domain of VASP*


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2PAVPDB entry 2PAV

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.4277.15150mM DL-malic acid pH 7.0, 18% PEG 3350, pH 7.4, VAPOR DIFFUSION, SITTING DROP, temperature 277.15K
Crystal Properties
Matthews coefficientSolvent content
2.0138.83

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 119.094α = 90
b = 56.589β = 104.75
c = 75.227γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray200CCDADSC QUANTUM 315mirrors2006-06-12MSINGLE 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
11.55097.50.0710.07141.97.3753937539310.87
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)
11.51.5598.30.2930.29397.57487

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 2PAV1.50131.777666576665385599.060.1580.1580.1560.19RANDOM10.847
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]
0.040.09-0.080.09
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.582
r_dihedral_angle_4_deg17.353
r_dihedral_angle_3_deg13.356
r_dihedral_angle_1_deg6.447
r_scangle_it4.118
r_scbond_it2.788
r_mcangle_it1.737
r_angle_refined_deg1.695
r_mcbond_it1.138
r_nbtor_refined0.317
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.582
r_dihedral_angle_4_deg17.353
r_dihedral_angle_3_deg13.356
r_dihedral_angle_1_deg6.447
r_scangle_it4.118
r_scbond_it2.788
r_mcangle_it1.737
r_angle_refined_deg1.695
r_mcbond_it1.138
r_nbtor_refined0.317
r_symmetry_vdw_refined0.25
r_nbd_refined0.229
r_xyhbond_nbd_refined0.2
r_symmetry_hbond_refined0.173
r_metal_ion_refined0.133
r_chiral_restr0.11
r_bond_refined_d0.015
r_gen_planes_refined0.008
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4049
Nucleic Acid Atoms
Solvent Atoms732
Heterogen Atoms32

Software

Software
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
SCALEPACKdata scaling
AMoREphasing