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Structure of NK cell receptor ligand CD48
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2PTT PDB ENTRY 2PTT
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.8 277 30% (w/v) PEG 8000, 100 mM sodium imidazole, 0.2 M NaCl, pH 7.8, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 1.88 34.49
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 78.87 α = 90 b = 78.87 β = 90 c = 31.258 γ = 90
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 2006-06-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X29A 1.0 NSLS X29A
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 1.66 50 97.3 0.047 66.7 12.9 11309 20.8
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) 1.66 1.72 81.5 0.2 8.4 9.4 1041
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 PDB ENTRY 2PTT 1.66 50 10720 538 97.4 0.20487 0.20212 0.2007 0.2615 0.2678 RANDOM 25.242
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] -1.42 -1.42 2.83
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.505 r_dihedral_angle_4_deg 30.602 r_dihedral_angle_3_deg 14.195 r_dihedral_angle_1_deg 6.098 r_scangle_it 4.699 r_scbond_it 3.158 r_mcangle_it 1.964 r_angle_refined_deg 1.761 r_mcbond_it 1.34 r_nbtor_refined 0.311
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.505 r_dihedral_angle_4_deg 30.602 r_dihedral_angle_3_deg 14.195 r_dihedral_angle_1_deg 6.098 r_scangle_it 4.699 r_scbond_it 3.158 r_mcangle_it 1.964 r_angle_refined_deg 1.761 r_mcbond_it 1.34 r_nbtor_refined 0.311 r_nbd_refined 0.242 r_symmetry_vdw_refined 0.166 r_xyhbond_nbd_refined 0.13 r_chiral_restr 0.127 r_symmetry_hbond_refined 0.094 r_bond_refined_d 0.018 r_gen_planes_refined 0.009 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 797 Nucleic Acid Atoms Solvent Atoms 81 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement HKL-2000 data collection HKL-2000 data reduction HKL-2000 data scaling PHASER phasing