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Nck1 SH2-domain in complex with a dodecaphosphopeptide from EPEC protein Tir
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details other NCK1-APO
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 TECHNIQUE: 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 coefficient Solvent content 2.26 45
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 55.092 α = 90 b = 60.518 β = 90 c = 65.061 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 2004-06-01 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 1.4 30 96.4 0.04 28.1 4 38419
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 1.4 1.42 88 0.31 4.2 3.7
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-APO 1.5 28.02 28813 1532 85.4 0.198 0.196 0.2041 0.235 0.2391 RANDOM 11.68
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 -0.09 0.04
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.809 r_dihedral_angle_4_deg 22.083 r_dihedral_angle_3_deg 12.252 r_dihedral_angle_1_deg 4.672 r_scangle_it 2.548 r_mcangle_it 2.473 r_angle_refined_deg 2.171 r_scbond_it 1.857 r_mcbond_it 1.703 r_angle_other_deg 1.572
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.809 r_dihedral_angle_4_deg 22.083 r_dihedral_angle_3_deg 12.252 r_dihedral_angle_1_deg 4.672 r_scangle_it 2.548 r_mcangle_it 2.473 r_angle_refined_deg 2.171 r_scbond_it 1.857 r_mcbond_it 1.703 r_angle_other_deg 1.572 r_nbd_refined 0.203 r_nbtor_refined 0.17 r_symmetry_vdw_other 0.169 r_nbd_other 0.16 r_symmetry_hbond_refined 0.137 r_symmetry_vdw_refined 0.13 r_xyhbond_nbd_refined 0.122 r_chiral_restr 0.111 r_nbtor_other 0.076 r_bond_refined_d 0.012 r_bond_other_d 0.007 r_gen_planes_refined 0.005 r_gen_planes_other 0.002 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 Atoms Number Protein Atoms 1825 Nucleic Acid Atoms Solvent Atoms 255 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling EPMR phasing