2BKI

Myosin VI nucleotide-free (MDinsert2-IQ) crystal structure


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1OE9PDB ENTRY 1OE9

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
18-10% PEG 8000, 50MM MES PH 6.7, 150MM NH4.SO4, 3% ISO-PROPANOL, 3% TERT-BUTANOL
Crystal Properties
Matthews coefficientSolvent content
3.9168.31

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 104.781α = 90
b = 250.167β = 90
c = 67.274γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC CCDMSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID23-1ESRFID23-1

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
12.940970.1216.36.3389612
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)
12.93.06970.443.7

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 1OE92.940361911948950.2660.2640.304RANDOM43.74
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]
-2.742.650.1
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg5.238
r_angle_other_deg2.037
r_scangle_it1.987
r_angle_refined_deg1.149
r_scbond_it1.129
r_mcangle_it0.965
r_mcbond_it0.517
r_symmetry_vdw_other0.226
r_nbd_other0.207
r_symmetry_hbond_refined0.202
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg5.238
r_angle_other_deg2.037
r_scangle_it1.987
r_angle_refined_deg1.149
r_scbond_it1.129
r_mcangle_it0.965
r_mcbond_it0.517
r_symmetry_vdw_other0.226
r_nbd_other0.207
r_symmetry_hbond_refined0.202
r_nbd_refined0.174
r_xyhbond_nbd_refined0.173
r_symmetry_vdw_refined0.164
r_nbtor_other0.081
r_chiral_restr0.064
r_bond_refined_d0.013
r_gen_planes_refined0.003
r_bond_other_d0.002
r_gen_planes_other0.002
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 Atoms7991
Nucleic Acid Atoms
Solvent Atoms49
Heterogen Atoms9

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing