1UJ0

Crystal Structure of STAM2 SH3 domain in complex with a UBPY-derived peptide


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP2770.08M Sodium Phosphate monobasic, 1.92M Potassium phosphate dibasic, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
2.2945.97

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 48.454α = 90
b = 48.454β = 90
c = 58.582γ = 120
Symmetry
Space GroupP 61

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU2002-10-02MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSPRING-8 BEAMLINE BL26B11.00SPring-8BL26B1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
11.734.197.985016
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
1.71.7996.8

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT1.734.118500760289897.620.21630.21630.214580.22966RANDOM25.802
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]
0.580.290.58-0.87
RMS Deviations
KeyRefinement Restraint Deviation
r_scangle_it5.352
r_dihedral_angle_1_deg5.23
r_scbond_it3.383
r_mcangle_it2.58
r_angle_refined_deg1.673
r_mcbond_it1.458
r_symmetry_vdw_refined0.27
r_symmetry_hbond_refined0.235
r_nbd_refined0.22
r_xyhbond_nbd_refined0.215
RMS Deviations
KeyRefinement Restraint Deviation
r_scangle_it5.352
r_dihedral_angle_1_deg5.23
r_scbond_it3.383
r_mcangle_it2.58
r_angle_refined_deg1.673
r_mcbond_it1.458
r_symmetry_vdw_refined0.27
r_symmetry_hbond_refined0.235
r_nbd_refined0.22
r_xyhbond_nbd_refined0.215
r_chiral_restr0.113
r_bond_refined_d0.021
r_gen_planes_refined0.009
r_bond_other_d
r_angle_other_deg
r_dihedral_angle_2_deg
r_dihedral_angle_3_deg
r_dihedral_angle_4_deg
r_gen_planes_other
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms548
Nucleic Acid Atoms
Solvent Atoms64
Heterogen Atoms5

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
CCP4data scaling
EPMRphasing