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Crystal structure of the human leukocyte-associated Ig-like receptor-1 (LAIR-1)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2GI7 Model from Swiss-model based on alignment with PDB entries 2GI7, 2D3V, 1UGN, 2GW5 experimental model PDB 2D3V Model from Swiss-model based on alignment with PDB entries 2GI7, 2D3V, 1UGN, 2GW5 experimental model PDB 1UGN Model from Swiss-model based on alignment with PDB entries 2GI7, 2D3V, 1UGN, 2GW5 experimental model PDB 2GW5 Model from Swiss-model based on alignment with PDB entries 2GI7, 2D3V, 1UGN, 2GW5
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 4.3 291 25-30% PEG-1500, 100mM succinic acid, 100mM sodium dihydrogen phosphate, 100mM glycine, 10mM CoCl2, pH 4.3, VAPOR DIFFUSION, SITTING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 2.14 42.58
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 69.395 α = 90 b = 69.395 β = 90 c = 54.258 γ = 120
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 315r 2007-10-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 1.0396 ESRF ID23-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 1.8 60.098 96.3 0.067 0.067 20.2 5.5 26097 -3.7 17.458
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.8 1.9 78.4 0.208 0.208 3.5 3.9 3098
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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 Model from Swiss-model based on alignment with PDB entries 2GI7, 2D3V, 1UGN, 2GW5 1.8 34.698 2.05 26079 1319 96.28 0.1242 0.124 0.123 0.157 0.232 random 23.233
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] 0.565 0.565 -1.752
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 16.379 f_angle_d 1.279 f_chiral_restr 0.079 f_bond_d 0.009 f_plane_restr 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2320 Nucleic Acid Atoms Solvent Atoms 443 Heterogen Atoms 11
Software Software Software Name Purpose MOSFLM data reduction SCALA data scaling PHENIX refinement PDB_EXTRACT data extraction MOLREP phasing