2CI9

Nck1 SH2-domain in complex with a dodecaphosphopeptide from EPEC protein Tir


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP8.5TECHNIQUE: HANGING-DROP, VAPOR-DIFFUSION PROTEIN CONCENTRATION: 8MG/ML PROTEIN:LIGAND = 1:1.1 RESERVOIRE: 2.4M (NH4)2HPO4, 0.1M TRIS, PH 8.5 CRYOCONDITIONS: 50% MPD
Crystal Properties
Matthews coefficientSolvent content
2.2645

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 55.092α = 90
b = 60.518β = 90
c = 65.061γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARRESEARCH2 AU-COATED X-RAY MIRRORS2004-06-01MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONMPG/DESY, HAMBURG BEAMLINE BW6MPG/DESY, HAMBURGBW6

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
11.43096.40.0428.1438419
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)
11.41.42880.314.23.7

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 REPLACEMENTTHROUGHOUTNCK1-APO1.528.0228813153285.40.1980.1960.235RANDOM11.68
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]
0.05-0.090.04
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.809
r_dihedral_angle_4_deg22.083
r_dihedral_angle_3_deg12.252
r_dihedral_angle_1_deg4.672
r_scangle_it2.548
r_mcangle_it2.473
r_angle_refined_deg2.171
r_scbond_it1.857
r_mcbond_it1.703
r_angle_other_deg1.572
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.809
r_dihedral_angle_4_deg22.083
r_dihedral_angle_3_deg12.252
r_dihedral_angle_1_deg4.672
r_scangle_it2.548
r_mcangle_it2.473
r_angle_refined_deg2.171
r_scbond_it1.857
r_mcbond_it1.703
r_angle_other_deg1.572
r_nbd_refined0.203
r_nbtor_refined0.17
r_symmetry_vdw_other0.169
r_nbd_other0.16
r_symmetry_hbond_refined0.137
r_symmetry_vdw_refined0.13
r_xyhbond_nbd_refined0.122
r_chiral_restr0.111
r_nbtor_other0.076
r_bond_refined_d0.012
r_bond_other_d0.007
r_gen_planes_refined0.005
r_gen_planes_other0.002
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
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_other
r_long_range_B_refined
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 Atoms1825
Nucleic Acid Atoms
Solvent Atoms255
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
EPMRphasing