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The High Resolution Crystal Structure of HLA-A1 Complexed with the MAGE-A1 Peptide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1W72 PDB ENTRY 1W72
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 291 20% PEG 3350, 0.2M Sodium Fluoride, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 2.68 54.14
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 51.176 α = 90 b = 74.06 β = 90 c = 125.94 γ = 90
Symmetry Space Group P 21 21 21
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 mirror 2005-05-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.1 0.954 BESSY 14.1
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 1.8 63.888 97 0.109 0.109 17.3 4.1 43828 18.248
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 1.8 1.9 95 0.351 0.351 3.82 4 6163
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 1W72 1.8 19.65 43728 2202 96.78 0.196 0.195 0.1924 0.225 0.2224 RANDOM 19.157
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] -0.61 1.06 -0.45
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.262 r_dihedral_angle_4_deg 19.26 r_dihedral_angle_3_deg 14.807 r_dihedral_angle_1_deg 5.949 r_scangle_it 3.913 r_scbond_it 2.541 r_mcangle_it 1.504 r_angle_refined_deg 1.451 r_mcbond_it 0.942 r_nbtor_refined 0.298
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.262 r_dihedral_angle_4_deg 19.26 r_dihedral_angle_3_deg 14.807 r_dihedral_angle_1_deg 5.949 r_scangle_it 3.913 r_scbond_it 2.541 r_mcangle_it 1.504 r_angle_refined_deg 1.451 r_mcbond_it 0.942 r_nbtor_refined 0.298 r_nbd_refined 0.203 r_symmetry_vdw_refined 0.19 r_xyhbond_nbd_refined 0.173 r_symmetry_hbond_refined 0.131 r_chiral_restr 0.102 r_bond_refined_d 0.015 r_gen_planes_refined 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3134 Nucleic Acid Atoms Solvent Atoms 587 Heterogen Atoms 18
Software Software Software Name Purpose MOSFLM data reduction SCALA data scaling MOLREP phasing REFMAC refinement PDB_EXTRACT data extraction ADSC data collection