2Q36

Actin Dimer Cross-linked between Residues 191 and 374 and complexed with Kabiramide C


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2A5Xpdb entry 2A5X

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP8.529830% PEG4000, 0.1 M Tris, 0.2 M lithium sulfate, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.652.63

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 40.539α = 90
b = 74.276β = 90
c = 144.474γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 3152005-10-21MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALS BEAMLINE 8.2.21.00ALS8.2.2

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
12.49901000.1128.87.91598715987-341.7
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)
12.492.5999.90.4197.61727

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 2A5X2.572.17157671576780099.980.1770.1770.1750.223RANDOM21.725
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]
-0.20.53-0.33
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.193
r_dihedral_angle_4_deg16.68
r_dihedral_angle_3_deg13.227
r_dihedral_angle_1_deg3.797
r_mcangle_it2.504
r_scangle_it2.432
r_mcbond_it1.681
r_scbond_it1.616
r_angle_refined_deg1.533
r_angle_other_deg0.885
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.193
r_dihedral_angle_4_deg16.68
r_dihedral_angle_3_deg13.227
r_dihedral_angle_1_deg3.797
r_mcangle_it2.504
r_scangle_it2.432
r_mcbond_it1.681
r_scbond_it1.616
r_angle_refined_deg1.533
r_angle_other_deg0.885
r_mcbond_other0.331
r_symmetry_vdw_other0.28
r_nbd_refined0.2
r_nbd_other0.19
r_nbtor_refined0.175
r_metal_ion_refined0.173
r_symmetry_vdw_refined0.157
r_xyhbond_nbd_refined0.143
r_symmetry_hbond_refined0.124
r_nbtor_other0.085
r_chiral_restr0.074
r_bond_refined_d0.008
r_gen_planes_refined0.003
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2817
Nucleic Acid Atoms
Solvent Atoms69
Heterogen Atoms109

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
BOSdata collection