1YV3

The structural basis of blebbistatin inhibition and specificity for myosin II


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1VOMpdb entry 1VOM

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7278100 mM MOPS (pH 7.0), 250 mM MgCl2, 11% PEG 8000, 1 mM TCEP, 2 mM Thymol, 1 mM MgCl2, 2 mM ADP, and 3 mM sodium vanadate, VAPOR DIFFUSION, HANGING DROP, temperature 278K
Crystal Properties
Matthews coefficientSolvent content
2.8256.01

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 88.106α = 90
b = 145.77β = 90
c = 152.912γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMAR CCD 165 mm2004-08-09MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 32-ID0.708APS32-ID

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
124099.80.062245.86347833.4
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)
22.0798.20.2693.75.163478

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)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 1VOM24063478338899.510.175140.175140.172980.21498RANDOM20.417
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]
0.290.51-0.8
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg5.928
r_scangle_it4.756
r_scbond_it3.059
r_mcangle_it2.072
r_angle_refined_deg1.685
r_mcbond_it1.174
r_angle_other_deg1.07
r_symmetry_vdw_other0.326
r_metal_ion_refined0.25
r_nbd_other0.248
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg5.928
r_scangle_it4.756
r_scbond_it3.059
r_mcangle_it2.072
r_angle_refined_deg1.685
r_mcbond_it1.174
r_angle_other_deg1.07
r_symmetry_vdw_other0.326
r_metal_ion_refined0.25
r_nbd_other0.248
r_nbd_refined0.226
r_symmetry_hbond_refined0.205
r_xyhbond_nbd_refined0.185
r_symmetry_vdw_refined0.126
r_chiral_restr0.116
r_nbtor_other0.089
r_bond_refined_d0.022
r_gen_planes_other0.013
r_gen_planes_refined0.011
r_bond_other_d0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5481
Nucleic Acid Atoms
Solvent Atoms678
Heterogen Atoms60

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
SCALEPACKdata scaling
MOLREPphasing