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TAP-A-associated rat MHC class I molecule
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1ED3 PDB ENTRY 1ED3 MOLECULE 1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 290 2M (NH4)2SO4, 1% glycerol, 0.1 M Tris/HCl, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 290K
Crystal Properties Matthews coefficient Solvent content 2.96 58.51
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 110.049 α = 90 b = 109.566 β = 90 c = 45.3 γ = 90
Symmetry Space Group P 21 21 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 IMAGE PLATE MARRESEARCH 1999-04-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL7-1 1.08 SSRL BL7-1
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 2.35 19.8 94.9 0.08 12.7 2.76 22313 -3 32.7
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 2.35 2.43 92 0.423 1.86 2.38 2120
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 1ED3 MOLECULE 1 2.35 19.8 21660 2156 97.16 0.24935 0.2473 0.2424 0.26803 0.2663 RANDOM 11.686
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] -1.12 5.96 -4.85
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 18.483 r_dihedral_angle_1_deg 3.077 r_scangle_it 1.978 r_angle_refined_deg 1.463 r_scbond_it 1.126 r_angle_other_deg 0.783 r_symmetry_hbond_refined 0.751 r_mcangle_it 0.614 r_mcbond_it 0.319 r_nbd_other 0.252
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 18.483 r_dihedral_angle_1_deg 3.077 r_scangle_it 1.978 r_angle_refined_deg 1.463 r_scbond_it 1.126 r_angle_other_deg 0.783 r_symmetry_hbond_refined 0.751 r_mcangle_it 0.614 r_mcbond_it 0.319 r_nbd_other 0.252 r_nbd_refined 0.249 r_symmetry_vdw_other 0.249 r_xyhbond_nbd_other 0.217 r_symmetry_vdw_refined 0.192 r_xyhbond_nbd_refined 0.176 r_chiral_restr 0.083 r_bond_refined_d 0.009 r_gen_planes_refined 0.005 r_gen_planes_other 0.002 r_bond_other_d 0.001 r_nbtor_other r_symmetry_hbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3149 Nucleic Acid Atoms Solvent Atoms 144 Heterogen Atoms 5
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling AMoRE phasing REFMAC refinement