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Large CDR3a loop alteration as a function of MHC mutation
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1LP9 PDB ENTRY 1LP9
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7.8 14% PEG 8000, 1 M NACL, 25 MM HEPES, PH 7.8
Crystal Properties Matthews coefficient Solvent content 2.55 51
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 93.489 α = 90 b = 84.178 β = 92.05 c = 121.773 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 MARRESEARCH MIRRORS 2005-03-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-BM APS 22-BM
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 2.4 30 83.9 0.06 8.3 2.76 76682
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 2.37 2.49 67.2 0.35 1.64 2.2
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 1LP9 2.4 121 59694 3142 84.8 0.243 0.24 0.2308 0.29 0.2758 RANDOM 36.94
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] 0.59 0.28 0.86 -1.43
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.832 r_dihedral_angle_4_deg 14.417 r_dihedral_angle_3_deg 13.284 r_dihedral_angle_1_deg 5.117 r_angle_refined_deg 1.04 r_scangle_it 0.79 r_scbond_it 0.535 r_mcangle_it 0.377 r_mcbond_it 0.301 r_nbtor_refined 0.292
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.832 r_dihedral_angle_4_deg 14.417 r_dihedral_angle_3_deg 13.284 r_dihedral_angle_1_deg 5.117 r_angle_refined_deg 1.04 r_scangle_it 0.79 r_scbond_it 0.535 r_mcangle_it 0.377 r_mcbond_it 0.301 r_nbtor_refined 0.292 r_symmetry_vdw_refined 0.277 r_symmetry_hbond_refined 0.192 r_nbd_refined 0.161 r_xyhbond_nbd_refined 0.109 r_chiral_restr 0.058 r_bond_refined_d 0.006 r_gen_planes_refined 0.002 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_mcangle_other r_scbond_other 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 13140 Nucleic Acid Atoms Solvent Atoms 210 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling REFMAC phasing