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Glycosylated form of human LLT1, a ligand for NKR-P1, in this structure forming hexamers
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3HUP
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.2 288 40%(v/v) PEG300 and 0.1M citrate phosphate buffer, pH 4.2, VAPOR DIFFUSION, HANGING DROP, temperature 288K
Crystal Properties Matthews coefficient Solvent content 2.3 46.43
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 70.06 α = 90 b = 70.06 β = 90 c = 101.71 γ = 120
Symmetry Space Group P 63 2 2
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 MARMOSAIC 225 mm CCD Si Mirror, double crystal Si monochromator, Rh mirror 2011-11-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.1 0.9184 BESSY 14.1
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 2.7 39 99.5 0.093 16.2 4.3 4431 4431 -3 66.1
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 2.7 2.76 99.3 0.757 2 4.4 273
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT throughout (except for the last cycle) 3HUP 2.75 39 4186 4186 223 99.52 0.23022 0.23022 0.22133 0.2314 0.2978 0.2329 RANDOM 40.052
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] -0.16 -0.08 -0.16 0.53
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.451 r_dihedral_angle_3_deg 21.562 r_dihedral_angle_4_deg 14.554 r_long_range_B_refined 10.195 r_long_range_B_other 10.192 r_dihedral_angle_1_deg 9.828 r_mcangle_it 6.515 r_mcangle_other 6.51 r_scangle_other 6.07 r_mcbond_it 3.959
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.451 r_dihedral_angle_3_deg 21.562 r_dihedral_angle_4_deg 14.554 r_long_range_B_refined 10.195 r_long_range_B_other 10.192 r_dihedral_angle_1_deg 9.828 r_mcangle_it 6.515 r_mcangle_other 6.51 r_scangle_other 6.07 r_mcbond_it 3.959 r_mcbond_other 3.957 r_scbond_it 3.78 r_scbond_other 3.777 r_angle_refined_deg 1.967 r_angle_other_deg 0.971 r_chiral_restr 0.108 r_bond_refined_d 0.018 r_gen_planes_refined 0.008 r_bond_other_d 0.006 r_gen_planes_other 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 945 Nucleic Acid Atoms Solvent Atoms 15 Heterogen Atoms 14
Software Software Software Name Purpose MxCuBE data collection BALBES phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling Sawaya data scaling