5Z05

Crystal structure of signalling protein from buffalo (SPB-40) with an acetone induced conformation of Trp78 at 1.49 A resolution


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.829835mM Tris -HCl pH- 8.0, 25mM Nacl, 20% Acetone.
Crystal Properties
Matthews coefficientSolvent content
2.6252.96

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 60.457α = 90
b = 66.517β = 90
c = 105.847γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARRESEARCHmirror2014-10-02MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE BM140.97ESRFBM14

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym 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
11.4956.32990.0311.44.26545020.4
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.491.53992.2

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 REPLACEMENTTHROUGHOUT5WSI1.4956.3265450347998.470.148560.147070.17641RANDOM26.13
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]
1.29-0.75-0.54
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.158
r_dihedral_angle_4_deg24.269
r_dihedral_angle_3_deg13.297
r_dihedral_angle_1_deg7.178
r_long_range_B_refined4.811
r_long_range_B_other4.811
r_scangle_other3.723
r_angle_refined_deg3.117
r_scbond_it2.536
r_scbond_other2.535
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.158
r_dihedral_angle_4_deg24.269
r_dihedral_angle_3_deg13.297
r_dihedral_angle_1_deg7.178
r_long_range_B_refined4.811
r_long_range_B_other4.811
r_scangle_other3.723
r_angle_refined_deg3.117
r_scbond_it2.536
r_scbond_other2.535
r_mcangle_other2.309
r_mcangle_it2.307
r_angle_other_deg1.84
r_mcbond_it1.672
r_mcbond_other1.667
r_chiral_restr0.191
r_bond_refined_d0.038
r_gen_planes_refined0.017
r_bond_other_d0.004
r_gen_planes_other0.002
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 Atoms2877
Nucleic Acid Atoms
Solvent Atoms413
Heterogen Atoms40

Software

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