☰ Navigation Tabs
Human receptor NKR-P1 in deglycosylated form, extracellular domain
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3T3A
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.2 294 20% (w/v) PEG 3350, 200 mM ammonium fluoride, 200 mM lithium chloride pH 6.2, protein concentration 12 mg/ml.
Crystal Properties Matthews coefficient Solvent content 2.13 42
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 44.806 α = 101.88 b = 68.404 β = 100.72 c = 101.564 γ = 100.64
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 1.9 48.68 97.9 0.085 0.999 12.9 7 87081 -3.7 24.6
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 1.9 1.93 95.1 0.894 0.671 1.7 6 4353
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 THROUGHOUT 3T3A 1.9 48.68 87080 4289 97.9 0.157 0.157 0.1667 0.207 0.1775 Random selection 32.031
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] -0.35 -0.98 0.66 -0.28 -2.05 1.6
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.689 r_dihedral_angle_4_deg 17.362 r_dihedral_angle_3_deg 13.342 r_long_range_B_refined 7.766 r_long_range_B_other 7.702 r_dihedral_angle_1_deg 7.099 r_scangle_other 5.843 r_mcangle_it 3.983 r_mcangle_other 3.983 r_scbond_it 3.782
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.689 r_dihedral_angle_4_deg 17.362 r_dihedral_angle_3_deg 13.342 r_long_range_B_refined 7.766 r_long_range_B_other 7.702 r_dihedral_angle_1_deg 7.099 r_scangle_other 5.843 r_mcangle_it 3.983 r_mcangle_other 3.983 r_scbond_it 3.782 r_scbond_other 3.782 r_mcbond_it 2.804 r_mcbond_other 2.804 r_angle_refined_deg 1.782 r_angle_other_deg 1.003 r_chiral_restr 0.11 r_bond_refined_d 0.018 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 8251 Nucleic Acid Atoms Solvent Atoms 682 Heterogen Atoms 224
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing