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human nck2 sh2-domain in complex with a decaphosphopeptide from translocated intimin receptor (tir) of epec
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details other NCK1-TIR
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 METHOD: 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 coefficient Solvent content 1.98 37.4
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 31.244 α = 90 b = 52.188 β = 90 c = 58.1 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD MARRESEARCH 2 AU COATED X-RAY MIRRORS 2004-05-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON MPG/DESY, HAMBURG BEAMLINE BW6 MPG/DESY, HAMBURG BW6
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 1.45 30 98.4 0.04 25.1 3.3 16143
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.45 1.48 97 0.31 3.7 2.9
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT NCK1-TIR 1.45 20.03 16142 879 98.5 0.15 0.149 0.1611 0.17 0.1805 RANDOM 14.3
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 Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.841 r_dihedral_angle_4_deg 19.188 r_dihedral_angle_3_deg 12.601 r_dihedral_angle_1_deg 4.725 r_scangle_it 3.958 r_mcangle_it 3.118 r_scbond_it 2.785 r_mcbond_it 2.285 r_angle_other_deg 1.907 r_angle_refined_deg 1.742
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.841 r_dihedral_angle_4_deg 19.188 r_dihedral_angle_3_deg 12.601 r_dihedral_angle_1_deg 4.725 r_scangle_it 3.958 r_mcangle_it 3.118 r_scbond_it 2.785 r_mcbond_it 2.285 r_angle_other_deg 1.907 r_angle_refined_deg 1.742 r_mcbond_other 0.582 r_symmetry_vdw_other 0.314 r_nbd_refined 0.217 r_nbd_other 0.214 r_xyhbond_nbd_refined 0.201 r_symmetry_vdw_refined 0.197 r_nbtor_refined 0.195 r_symmetry_hbond_refined 0.17 r_nbtor_other 0.13 r_chiral_restr 0.113 r_bond_refined_d 0.02 r_gen_planes_refined 0.007 r_bond_other_d 0.004 r_gen_planes_other 0.003 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 Atoms Number Protein Atoms 871 Nucleic Acid Atoms Solvent Atoms 103 Heterogen Atoms 10
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling EPMR phasing