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COMPLEX OF A B2 CHICKEN MHC CLASS I MOLECULE AND A 9MER CHICKEN PEPTIDE
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2YF6 PDB ENTRY 2YF6
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7 0.1M MMT BUFFER, PH 7.0, 25% W/V PEG 1500
Crystal Properties Matthews coefficient Solvent content 4.03 69.51
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 173.85 α = 90 b = 173.85 β = 90 c = 87.51 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 315 2011-12-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 Diamond I04
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 3.3 75.66 100 0.16 11.1 7.3 22882 1
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 3.3 3.56 99.9 0.56 3.8 7.5
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 2YF6 3.3 75.66 21707 1150 99.93 0.23804 0.23681 0.26168 0.2083 RANDOM 76.988
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] 30.13 30.13 -60.26
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 25.962 r_dihedral_angle_3_deg 14.702 r_dihedral_angle_4_deg 14.338 r_dihedral_angle_1_deg 3.759 r_angle_refined_deg 0.759 r_angle_other_deg 0.699 r_mcangle_it 0.416 r_mcbond_it 0.217 r_mcbond_other 0.217 r_scbond_it 0.069
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 25.962 r_dihedral_angle_3_deg 14.702 r_dihedral_angle_4_deg 14.338 r_dihedral_angle_1_deg 3.759 r_angle_refined_deg 0.759 r_angle_other_deg 0.699 r_mcangle_it 0.416 r_mcbond_it 0.217 r_mcbond_other 0.217 r_scbond_it 0.069 r_chiral_restr 0.047 r_bond_refined_d 0.004 r_gen_planes_refined 0.003 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcangle_other r_scbond_other r_scangle_it r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6052 Nucleic Acid Atoms Solvent Atoms 8 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing