3HPB

Crystal structure of SNX5-PX domain in P212121 space group


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
18277the protein solution in the final superdex-75 buffer (20 mM Tris.HCl, 100 mM NaCl, 0.02% NaN3, pH 8.0) was concentrated to 8 mg/ml. The Se-Met derivative and the 2.19 A crystals were obtained using an optimized initial crystallization condition of 8 ul of protein vs 1 ul of reservoir solution (0.2M (NH4)2SO4, 0.1M Sodium cacodylate tryhydrate pH 6.5, 30% PEG 8000) at 4C by sitting drop vapor diffusion, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
3.3959.25

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 42.957α = 90
b = 75.874β = 90
c = 77.512γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRIGAKU SATURN 944MIRRORS2006-10-17MSINGLE WAVELENGTH
21x-ray100CCDMARMOSAIC 300 mm CCDROSENBAUM-ROCK MONOCHROMATOR HIGH-RESOLUTION DOUBLE-CRYSTAL SI(220) SAGITTAL FO CUSING, ROSENBAUM- ROCK VERTICAL FOCUSING MIRROR2008-11-18MMAD
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU FR-E SUPERBRIGHT
2SYNCHROTRONAPS BEAMLINE 22-ID0.9793,0.9795,0.9718APS22-ID

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
1,22.1928.7893.40.03328.14.18126803
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)
2.192.2762.30.2563.52.05

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 DIFFRACTIONMADTHROUGHOUT2.1928.7811436124493.30.240.2360.284RANDOM48.12
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]
-1.190.151.04
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg43.298
r_dihedral_angle_4_deg23.943
r_dihedral_angle_3_deg16.213
r_dihedral_angle_1_deg5.259
r_scangle_it3.663
r_scbond_it2.156
r_mcangle_it1.324
r_angle_refined_deg1.284
r_mcbond_it0.682
r_chiral_restr0.101
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg43.298
r_dihedral_angle_4_deg23.943
r_dihedral_angle_3_deg16.213
r_dihedral_angle_1_deg5.259
r_scangle_it3.663
r_scbond_it2.156
r_mcangle_it1.324
r_angle_refined_deg1.284
r_mcbond_it0.682
r_chiral_restr0.101
r_bond_refined_d0.012
r_gen_planes_refined0.008
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_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1274
Nucleic Acid Atoms
Solvent Atoms135
Heterogen Atoms1

Software

Software
Software NamePurpose
StructureStudiodata collection
SnBphasing
PHASERphasing
REFMACrefinement
d*TREKdata reduction
d*TREKdata scaling