1OE9

Crystal structure of Myosin V motor with essential light chain-nucleotide-free


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2MYSPDB ENTRY 2MYS

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
16.56% PEG8000 (W/V), 50MM MOPS PH 6.5, 2MM DTT, 2MM NAN3
Crystal Properties
Matthews coefficientSolvent content
2.847.8

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 53.933α = 90
b = 98.247β = 101.43
c = 111.378γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray1002002-11-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID29ESRFID29

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
12.054096.80.06142.9691153
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)
12.052.1288.40.3352.342

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 2MYS2.054065624347496.80.2220.220.264RANDOM39.16
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]
1.120.22-0.91-0.12
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg5.388
r_scangle_it3.416
r_scbond_it2.067
r_mcangle_it1.509
r_angle_refined_deg1.3
r_mcbond_it0.823
r_angle_other_deg0.791
r_symmetry_vdw_other0.256
r_nbd_other0.237
r_nbd_refined0.203
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg5.388
r_scangle_it3.416
r_scbond_it2.067
r_mcangle_it1.509
r_angle_refined_deg1.3
r_mcbond_it0.823
r_angle_other_deg0.791
r_symmetry_vdw_other0.256
r_nbd_other0.237
r_nbd_refined0.203
r_xyhbond_nbd_refined0.195
r_symmetry_hbond_refined0.181
r_symmetry_vdw_refined0.135
r_nbtor_other0.085
r_chiral_restr0.08
r_bond_refined_d0.014
r_gen_planes_refined0.006
r_gen_planes_other0.003
r_bond_other_d0.002
r_dihedral_angle_2_deg
r_dihedral_angle_3_deg
r_dihedral_angle_4_deg
r_nbtor_refined
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 Atoms6919
Nucleic Acid Atoms
Solvent Atoms333
Heterogen Atoms5

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing