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T Cell Immunoglobulin Mucin-3 Crystal Structure Revealed a Galectin-9-independent Binding Surface
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1EAJ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5 291 1.8 M Ammonium Sulfate, 0.1 M Sodium Citrate pH 5.0, VAPOR DIFFUSION, SITTING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 1.87 34.19
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 23 α = 90 b = 52.809 β = 100.94 c = 38.941 γ = 90
Symmetry Space Group P 1 21 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 CCD ADSC QUANTUM 315 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X29A 1.4503 NSLS X29A
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 1.95 30 96.2 0.073 0.081 12 3.6 6457 6457
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 1.95 2.02 72.6 0.136 0.141 6.8 2.9 470
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 (All) 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 1eaj 1.952 30 6442 6442 305 96.09 0.158 0.158 0.156 0.1571 0.2 0.2025 RANDOM 20.153
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] -0.98 0.38 -0.94 2.07
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.719 r_dihedral_angle_4_deg 23.543 r_dihedral_angle_3_deg 15.006 r_dihedral_angle_1_deg 6.154 r_scangle_it 3.038 r_scbond_it 1.797 r_angle_refined_deg 1.195 r_mcangle_it 1.159 r_mcbond_it 0.638 r_nbtor_refined 0.303
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.719 r_dihedral_angle_4_deg 23.543 r_dihedral_angle_3_deg 15.006 r_dihedral_angle_1_deg 6.154 r_scangle_it 3.038 r_scbond_it 1.797 r_angle_refined_deg 1.195 r_mcangle_it 1.159 r_mcbond_it 0.638 r_nbtor_refined 0.303 r_nbd_refined 0.193 r_symmetry_vdw_refined 0.184 r_symmetry_hbond_refined 0.149 r_xyhbond_nbd_refined 0.139 r_chiral_restr 0.077 r_bond_refined_d 0.01 r_gen_planes_refined 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 866 Nucleic Acid Atoms Solvent Atoms 96 Heterogen Atoms 5
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction CBASS data collection HKL-2000 data reduction MOLREP phasing