2Q0U

Structure of Pectenotoxin-2 and Latrunculin B Bound to Actin


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2ASO 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP5.5293100 mM Na/MES/acetate, pH 5.5, 15% methyl ether poly(ethylene glycol) 5000, 10% hexanediol, 100 mM CaCl2, and 1 mM TCEP, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
1.9837.9

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 57.683α = 90
b = 54.342β = 90.27
c = 105.895γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDSBCRosenbaum-Rock double-crystal monochromator: Water cooled; sagitally focusing 2nd crystal, Rosenbaum-Rock vertical focusing mirror2006-08-06MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 19-BM0.96411APS19-BM

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
11.415096.60.0410.14.66088319
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)
1.411.4684.90.1365.74.15315

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 REPLACEMENTTHROUGHOUT2ASO1.454556889289197.810.1660.1650.181RANDOM11.813
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]
0.350.06-0.14-0.21
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.015
r_dihedral_angle_4_deg18.164
r_dihedral_angle_3_deg11.183
r_dihedral_angle_1_deg5.411
r_scangle_it2.14
r_angle_refined_deg1.678
r_scbond_it1.59
r_angle_other_deg1.164
r_mcangle_it1.075
r_mcbond_it0.664
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.015
r_dihedral_angle_4_deg18.164
r_dihedral_angle_3_deg11.183
r_dihedral_angle_1_deg5.411
r_scangle_it2.14
r_angle_refined_deg1.678
r_scbond_it1.59
r_angle_other_deg1.164
r_mcangle_it1.075
r_mcbond_it0.664
r_symmetry_hbond_refined0.239
r_nbd_refined0.224
r_symmetry_vdw_refined0.208
r_nbd_other0.191
r_symmetry_vdw_other0.184
r_nbtor_refined0.179
r_chiral_restr0.173
r_xyhbond_nbd_refined0.153
r_mcbond_other0.135
r_symmetry_metal_ion_refined0.096
r_nbtor_other0.085
r_metal_ion_refined0.082
r_gen_planes_refined0.01
r_bond_refined_d0.008
r_gen_planes_other0.003
r_bond_other_d0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2717
Nucleic Acid Atoms
Solvent Atoms357
Heterogen Atoms121

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-3000data collection
HKL-3000data reduction