☰ Navigation Tabs
Crystal structure of the human natural killer cell inhibitory receptor KIR2DL1 bound to its MHC ligand HLA-Cw4
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1QQD PDB entry 1QQD PDB entry 1NKR experimental model PDB 1NKR PDB entry 1QQD PDB entry 1NKR
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 277 PEG6000, magnesium chloride, ethylene glycol, N-(2-acetamindo)iminodiacetic acid , pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 3.8 67.59
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 213.631 α = 90 b = 75.867 β = 120.96 c = 125.746 γ = 90
Symmetry Space Group C 1 2 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 95 CCD BRANDEIS - B4 2000-01-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X25 1.1 NSLS X25
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 2.8 30 97.9 0.073 0.073 10.2 4 41881 41881 48.8
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 2.8 2.9 82.3 0.191 0.191 3 2 3503
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB entry 1QQD
PDB entry 1NKR 2.8 29.21 41881 41881 4229 97.8 0.2185 0.213 0.213 0.256 RANDOM 45.9
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] 2.06 15.6 -0.44 -1.62
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 25.6 c_angle_deg 1.4 c_improper_angle_d 0.85 c_bond_d 0.007 c_bond_d_na c_bond_d_prot c_angle_d c_angle_d_na c_angle_d_prot c_angle_deg_na
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 25.6 c_angle_deg 1.4 c_improper_angle_d 0.85 c_bond_d 0.007 c_bond_d_na c_bond_d_prot c_angle_d c_angle_d_na c_angle_d_prot c_angle_deg_na c_angle_deg_prot c_dihedral_angle_d_na c_dihedral_angle_d_prot c_improper_angle_d_na c_improper_angle_d_prot c_mcbond_it c_mcangle_it c_scbond_it c_scangle_it
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7858 Nucleic Acid Atoms Solvent Atoms 238 Heterogen Atoms
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling AMoRE phasing CNS refinement