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Structure of NKG2A/CD94 bound to HLA-E
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1KPR 1KPR, 1B6E experimental model PDB 1B6E 1KPR, 1B6E
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 291 1.8M ammonium sulfate, 0.3-0.7% sucrose, 100 mM Tris (8.0), VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 5.95 79.31
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 345.983 α = 90 b = 345.983 β = 90 c = 345.983 γ = 90
Symmetry Space Group I 41 3 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 103 CCD ADSC QUANTUM 315 2006-09-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 8.2.2 ALS 8.2.2
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 4.41 70 100 0.166 6.9 34.4 22619
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 4.4 4.56 100 0.489 1.03 26.3 2189
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-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1KPR, 1B6E 4.41 67.88 22600 21445 1155 99.95 0.32054 0.311 0.35529 0.3472 RANDOM 97.161
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.601 r_dihedral_angle_3_deg 18.979 r_dihedral_angle_4_deg 13.292 r_dihedral_angle_1_deg 6.202 r_angle_refined_deg 1.088 r_angle_other_deg 0.84 r_symmetry_vdw_other 0.257 r_scangle_it 0.251 r_nbd_refined 0.209 r_symmetry_vdw_refined 0.206
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.601 r_dihedral_angle_3_deg 18.979 r_dihedral_angle_4_deg 13.292 r_dihedral_angle_1_deg 6.202 r_angle_refined_deg 1.088 r_angle_other_deg 0.84 r_symmetry_vdw_other 0.257 r_scangle_it 0.251 r_nbd_refined 0.209 r_symmetry_vdw_refined 0.206 r_nbd_other 0.205 r_nbtor_refined 0.182 r_scbond_it 0.168 r_xyhbond_nbd_refined 0.162 r_mcangle_it 0.126 r_mcbond_it 0.089 r_nbtor_other 0.082 r_chiral_restr 0.066 r_mcbond_other 0.029 r_xyhbond_nbd_other 0.028 r_symmetry_hbond_refined 0.028 r_bond_refined_d 0.009 r_gen_planes_refined 0.003 r_bond_other_d 0.002 r_gen_planes_other 0.001 r_metal_ion_refined r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 10146 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling AMoRE phasing