2CIA

human nck2 sh2-domain in complex with a decaphosphopeptide from translocated intimin receptor (tir) of epec


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7METHOD: HANGING-DROP, VAPOUR-DIFFUSION PROTEIN CONCENTRATION: 8 MG/ML PROTEIN:LIGAND = 1:1.1 RESERVOIRE: 50% MPD, 15% ETHANOL, 0.01 M NA2 ACETATE, pH 7.00
Crystal Properties
Matthews coefficientSolvent content
1.9837.4

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 31.244α = 90
b = 52.188β = 90
c = 58.1γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARRESEARCH2 AU COATED X-RAY MIRRORS2004-05-17MSINGLE 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
11.453098.40.0425.13.316143
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)
11.451.48970.313.72.9

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-TIR1.4520.031614287998.50.150.1490.17RANDOM14.3
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]
0.03-0.01-0.02
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.841
r_dihedral_angle_4_deg19.188
r_dihedral_angle_3_deg12.601
r_dihedral_angle_1_deg4.725
r_scangle_it3.958
r_mcangle_it3.118
r_scbond_it2.785
r_mcbond_it2.285
r_angle_other_deg1.907
r_angle_refined_deg1.742
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.841
r_dihedral_angle_4_deg19.188
r_dihedral_angle_3_deg12.601
r_dihedral_angle_1_deg4.725
r_scangle_it3.958
r_mcangle_it3.118
r_scbond_it2.785
r_mcbond_it2.285
r_angle_other_deg1.907
r_angle_refined_deg1.742
r_mcbond_other0.582
r_symmetry_vdw_other0.314
r_nbd_refined0.217
r_nbd_other0.214
r_xyhbond_nbd_refined0.201
r_symmetry_vdw_refined0.197
r_nbtor_refined0.195
r_symmetry_hbond_refined0.17
r_nbtor_other0.13
r_chiral_restr0.113
r_bond_refined_d0.02
r_gen_planes_refined0.007
r_bond_other_d0.004
r_gen_planes_other0.003
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_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 Atoms871
Nucleic Acid Atoms
Solvent Atoms103
Heterogen Atoms10

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
EPMRphasing