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Monomeric form of human LLT1, a ligand for NKR-P1
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4QKJ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 3.5 294 2M ammonium sulfate, 0.1M sodium citrate, pH 3.5, VAPOR DIFFUSION, SITTING DROP, temperature 294K
Crystal Properties Matthews coefficient Solvent content 2.18 43.68
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 47.298 α = 90 b = 47.298 β = 90 c = 106.137 γ = 120
Symmetry Space Group P 32 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 100 CCD ADSC QUANTUM 315 Kirkpatrick Baez mirror pair 2012-03-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I02 0.9796 Diamond I02
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 1.95 50 99.7 0.074 21.2 6.3 10555 10555 -3 34
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 1.95 1.98 100 0.599 2.9 6.6 506
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 (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT throughout (except for the last cycle) 4QKJ 1.95 40.96 10529 10029 500 99.71 0.20138 0.20138 0.1939 0.247 0.241 random 39.755
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] -0.37 -0.37 -0.37 1.19
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 27.796 r_dihedral_angle_3_deg 15.138 r_dihedral_angle_4_deg 12.996 r_long_range_B_refined 9.016 r_long_range_B_other 8.921 r_dihedral_angle_1_deg 7.717 r_scangle_other 7.006 r_mcangle_it 5.096 r_mcangle_other 5.092 r_scbond_it 4.645
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 27.796 r_dihedral_angle_3_deg 15.138 r_dihedral_angle_4_deg 12.996 r_long_range_B_refined 9.016 r_long_range_B_other 8.921 r_dihedral_angle_1_deg 7.717 r_scangle_other 7.006 r_mcangle_it 5.096 r_mcangle_other 5.092 r_scbond_it 4.645 r_scbond_other 4.622 r_mcbond_it 3.612 r_mcbond_other 3.61 r_angle_refined_deg 1.933 r_angle_other_deg 0.942 r_chiral_restr 0.119 r_bond_refined_d 0.016 r_gen_planes_refined 0.008 r_bond_other_d 0.002 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 883 Nucleic Acid Atoms Solvent Atoms 42 Heterogen Atoms 19
Software Software Software Name Purpose ADSC data collection MOLREP phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling