2VAC

Structure of N-terminal Actin Depolymerizing Factor homology (ADF-H) domain of human twinfilin-2


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
180.01M ZINC CHLORIDE,10% ETHYLENE GLYCOL,20% PEG6000, 0.1M TRIS PH8.0
Crystal Properties
Matthews coefficientSolvent content
2.0138.8

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 35.817α = 90
b = 48.56β = 90
c = 70.127γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU IMAGE PLATEMULTI-LAYER VARIMAX HR2007-08-02MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU FR-E

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge 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
11.720.197.50.0724.46.81365318.66
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.71.7994.90.542.56.6

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 1M4J1.7201297167897.20.1720.170.214RANDOM15.83
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]
-0.31-0.721.03
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.356
r_dihedral_angle_4_deg15.983
r_dihedral_angle_3_deg11.424
r_dihedral_angle_1_deg6.275
r_scangle_it6.23
r_scbond_it5.001
r_mcangle_it2.978
r_mcbond_it2.775
r_angle_other_deg1.811
r_angle_refined_deg1.29
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.356
r_dihedral_angle_4_deg15.983
r_dihedral_angle_3_deg11.424
r_dihedral_angle_1_deg6.275
r_scangle_it6.23
r_scbond_it5.001
r_mcangle_it2.978
r_mcbond_it2.775
r_angle_other_deg1.811
r_angle_refined_deg1.29
r_symmetry_vdw_other0.302
r_nbd_refined0.208
r_nbd_other0.199
r_symmetry_vdw_refined0.18
r_nbtor_refined0.173
r_symmetry_hbond_refined0.157
r_xyhbond_nbd_refined0.123
r_nbtor_other0.096
r_chiral_restr0.085
r_bond_refined_d0.013
r_gen_planes_refined0.005
r_bond_other_d0.003
r_gen_planes_other0.001
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_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1065
Nucleic Acid Atoms
Solvent Atoms161
Heterogen Atoms7

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing