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Human receptor NKR-P1 in glycosylated form, extracellular domain
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3FF7
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.2 294 20% (w/v) PEG 3350, 200 mM di-sodium tartrate pH 7.2
PROTEIN CONCENTRATION 20 MG/ML
Crystal Properties Matthews coefficient Solvent content 2.32 47
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 68.241 α = 90 b = 68.241 β = 90 c = 127.195 γ = 120
Symmetry Space Group P 31 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 PIXEL DECTRIS PILATUS3 6M 2015-05-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.97625 Diamond I03
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) CC (Half) 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 43.3 100 0.061 1 41 39.5 32555 -3.7 25.3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.8 1.84 100 0.637 0.975 7.4 40.5 1900
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) 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 FREE R-VALUE 3ff7 1.8 43.3 32508 1580 99.99 0.168 0.167 0.1767 0.202 0.1787 random 33.5
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] 0.11 0.05 0.11 -0.34
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.354 r_dihedral_angle_4_deg 15.6 r_dihedral_angle_3_deg 11.997 r_long_range_B_refined 8.22 r_long_range_B_other 8.192 r_dihedral_angle_1_deg 6.891 r_scangle_other 6.275 r_scbond_it 4.018 r_scbond_other 4.018 r_mcangle_it 3.932
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.354 r_dihedral_angle_4_deg 15.6 r_dihedral_angle_3_deg 11.997 r_long_range_B_refined 8.22 r_long_range_B_other 8.192 r_dihedral_angle_1_deg 6.891 r_scangle_other 6.275 r_scbond_it 4.018 r_scbond_other 4.018 r_mcangle_it 3.932 r_mcangle_other 3.93 r_mcbond_it 2.83 r_mcbond_other 2.783 r_angle_refined_deg 1.736 r_angle_other_deg 0.976 r_chiral_restr 0.107 r_bond_refined_d 0.016 r_gen_planes_refined 0.009 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 2050 Nucleic Acid Atoms Solvent Atoms 225 Heterogen Atoms 172
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling BALBES phasing