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Crystal structure of HA-1 minor histocompatibility antigen bound to human class I MHC HLA-A2
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1BD2 PDB ENTRY 1BD2
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7.5 298 20 % PEG 10K, 0.1 M HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K, pH 7.50
Crystal Properties Matthews coefficient Solvent content 2.52 51.27
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 53.17 α = 90 b = 80.98 β = 112.32 c = 56.26 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 ADSC 2005-11-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-4 ESRF ID14-4
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 1.3 42.033 99.5 0.064 0.064 7.8 4 108069
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) 1.3 1.37 100 0.583 0.583 1.3 4
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) 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 FREE R PDB ENTRY 1BD2 1.3 20 108030 5421 94.9 0.169 0.2045 0.204 0.2211 RANDOM 20.552
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]
RMS Deviations Key Refinement Restraint Deviation s_non_zero_chiral_vol 0.073 s_approx_iso_adps 0.072 s_zero_chiral_vol 0.051 s_similar_adp_cmpnt 0.051 s_angle_d 0.029 s_from_restr_planes 0.027 s_anti_bump_dis_restr 0.019 s_bond_d 0.012 s_rigid_bond_adp_cmpnt 0.004 s_similar_dist
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3154 Nucleic Acid Atoms Solvent Atoms 354 Heterogen Atoms
Software Software Software Name Purpose SCALA data processing SHELX refinement PDB_EXTRACT data extraction MOSFLM data reduction SCALA data scaling CNS phasing SHELXL-97 refinement