3WWV

C-terminal domain of stomatin operon partner protein 1510-C from Pyrococcus horikoshii


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.529320% Jeffamine M-600, 0.1M HEPES-NaOH, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
1.9737.63

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 75.847α = 90
b = 75.847β = 90
c = 43.631γ = 120
Symmetry
Space GroupP 62 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray95CCDADSC QUANTUM 315rmirror2013-02-16MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPHOTON FACTORY BEAMLINE BL-17A0.9800Photon FactoryBL-17A

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
12.419.5799.70.07725.910316527.6
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)
12.42.531000.4046.910.5443

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 2EXD2.418.96286528899.370.224640.220840.25796RANDOM31.797
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]
0.050.030.05-0.17
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.748
r_dihedral_angle_4_deg21.193
r_dihedral_angle_3_deg15.518
r_dihedral_angle_1_deg6.808
r_long_range_B_refined6.385
r_mcangle_it2.895
r_scbond_it2.209
r_mcbond_it1.649
r_angle_refined_deg1.316
r_chiral_restr0.076
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.748
r_dihedral_angle_4_deg21.193
r_dihedral_angle_3_deg15.518
r_dihedral_angle_1_deg6.808
r_long_range_B_refined6.385
r_mcangle_it2.895
r_scbond_it2.209
r_mcbond_it1.649
r_angle_refined_deg1.316
r_chiral_restr0.076
r_bond_refined_d0.007
r_gen_planes_refined0.003
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
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_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_it
r_scangle_other
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 Atoms507
Nucleic Acid Atoms
Solvent Atoms20
Heterogen Atoms1

Software

Software
Software NamePurpose
XDSdata scaling
PHENIXmodel building
REFMACrefinement
XDSdata reduction
SCALAdata scaling
PHENIXphasing