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Dimeric form of human LLT1, a ligand for NKR-P1
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, SITTING DROP 7 294 30%(w/v) polyethylene glycol 6000, 0.1M HEPES, pH 7.0 , VAPOR DIFFUSION, SITTING DROP, temperature 294K
Crystal Properties Matthews coefficient Solvent content 1.93 36.17
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 50.87 α = 90 b = 57.82 β = 90 c = 82.25 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 PIXEL DECTRIS PILATUS 2M Kirkpatrick Baez mirror pair 2012-06-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 0.9200 Diamond I04-1
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 1.8 47.3 91.8 0.093 11.3 8.3 21104 21104 -3.7 20.7
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 1.8 1.84 81 0.462 3 5.4 1087
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 1.8 47.3 21045 21045 1104 90.91 0.18041 0.18041 0.17499 0.1886 0.24992 0.2076 random 27.584
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] -0.39 1.14 -0.75
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.55 r_dihedral_angle_4_deg 15.813 r_dihedral_angle_3_deg 15.024 r_dihedral_angle_1_deg 7.259 r_long_range_B_refined 6.546 r_long_range_B_other 6.34 r_scangle_other 4.28 r_mcangle_it 3.56 r_mcangle_other 3.56 r_scbond_it 2.75
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.55 r_dihedral_angle_4_deg 15.813 r_dihedral_angle_3_deg 15.024 r_dihedral_angle_1_deg 7.259 r_long_range_B_refined 6.546 r_long_range_B_other 6.34 r_scangle_other 4.28 r_mcangle_it 3.56 r_mcangle_other 3.56 r_scbond_it 2.75 r_scbond_other 2.749 r_mcbond_it 2.425 r_mcbond_other 2.424 r_angle_refined_deg 1.702 r_angle_other_deg 0.933 r_chiral_restr 0.107 r_bond_refined_d 0.016 r_gen_planes_refined 0.008 r_bond_other_d 0.003 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 1987 Nucleic Acid Atoms Solvent Atoms 214 Heterogen Atoms 56
Software Software Software Name Purpose BALBES phasing REFMAC refinement MOSFLM data reduction Aimless data scaling