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Crystal Structure of Mouse Triggering Receptor Expressed on Myeloid Cells 1 (TREM-1) at 1.76
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1SMO pdb entry 1SMO
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6 277 MES, PEG 8000, zinc acetate, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.9 57.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 47.837 α = 90 b = 49.081 β = 90 c = 125.208 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 93 CCD ADSC QUANTUM 315 Flat mirror (vertical focusing), single crystal Si(111) bent monochromator (horizontal focusing) 2004-06-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL11-1 0.97954 SSRL BL11-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.76 31.47 98.3 0.129 39.8 6.3 30078 29567
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.76 1.79 87.2 0.595 2.5 3.6 1269
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-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 1SMO 1.76 31.47 27356 26009 1346 93.04 0.22614 0.22497 0.2392 0.24841 0.2686 RANDOM 22.45
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] -0.1 -0.02 0.12
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 6.99 r_scangle_it 4.881 r_scbond_it 3.011 r_mcangle_it 1.73 r_angle_refined_deg 1.675 r_mcbond_it 0.926 r_angle_other_deg 0.814 r_symmetry_hbond_refined 0.543 r_symmetry_vdw_refined 0.304 r_nbd_other 0.247
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 6.99 r_scangle_it 4.881 r_scbond_it 3.011 r_mcangle_it 1.73 r_angle_refined_deg 1.675 r_mcbond_it 0.926 r_angle_other_deg 0.814 r_symmetry_hbond_refined 0.543 r_symmetry_vdw_refined 0.304 r_nbd_other 0.247 r_nbd_refined 0.212 r_metal_ion_refined 0.151 r_xyhbond_nbd_refined 0.123 r_symmetry_vdw_other 0.101 r_chiral_restr 0.1 r_nbtor_other 0.088 r_bond_refined_d 0.02 r_gen_planes_other 0.011 r_gen_planes_refined 0.009 r_bond_other_d 0.002 r_dihedral_angle_2_deg r_dihedral_angle_3_deg r_dihedral_angle_4_deg r_nbtor_refined r_xyhbond_nbd_other r_metal_ion_other r_symmetry_hbond_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 1784 Nucleic Acid Atoms Solvent Atoms 59 Heterogen Atoms 3
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling PHASER phasing