4D81

Metallosphera sedula Vps4 crystal structure


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
18.840% (W/V) POLYETHYLENE GLYCOL 200 (PEG200) 100 MM TRIS-HCL BUFFER (PH 8.8)
Crystal Properties
Matthews coefficientSolvent content
2.1542.78

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 65.269α = 90
b = 65.269β = 90
c = 112.521γ = 120
Symmetry
Space GroupP 65

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARRESEARCH2013-11-11MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE BM14ESRFBM14

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
12.456.599.70.0616.74.1129352
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)
12.42.4999.70.632.34.2

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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 REPLACEMENTTHROUGHOUT2.456.521003856599.630.209710.206650.26283RANDOM55.263
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]
0.660.330.66-2.13
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.621
r_dihedral_angle_3_deg16.628
r_dihedral_angle_4_deg10.494
r_long_range_B_refined9.434
r_long_range_B_other9.434
r_scangle_other7.2
r_dihedral_angle_1_deg5.806
r_mcangle_it5.63
r_mcangle_other5.63
r_scbond_it4.646
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.621
r_dihedral_angle_3_deg16.628
r_dihedral_angle_4_deg10.494
r_long_range_B_refined9.434
r_long_range_B_other9.434
r_scangle_other7.2
r_dihedral_angle_1_deg5.806
r_mcangle_it5.63
r_mcangle_other5.63
r_scbond_it4.646
r_scbond_other4.644
r_mcbond_it3.867
r_mcbond_other3.857
r_angle_refined_deg1.572
r_angle_other_deg0.83
r_chiral_restr0.085
r_bond_refined_d0.012
r_gen_planes_refined0.006
r_bond_other_d0.002
r_gen_planes_other0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2111
Nucleic Acid Atoms
Solvent Atoms7
Heterogen Atoms27

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALAdata scaling
PHASERphasing