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Crystal structure of HLA-A1:MAGE-A1 in complex with Fab-Hyb3
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1DUZ PDB ENTRIES 1DUZ, 7FAB, 2GFB, 2FB4 experimental model PDB 7FAB PDB ENTRIES 1DUZ, 7FAB, 2GFB, 2FB4 experimental model PDB 2GFB PDB ENTRIES 1DUZ, 7FAB, 2GFB, 2FB4 experimental model PDB 2FB4 PDB ENTRIES 1DUZ, 7FAB, 2GFB, 2FB4
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 6.5 MES PH 6.5, NACL 600MM, 19% PEG3350, 80MM DIOXANE
Crystal Properties Matthews coefficient Solvent content 2.1 42
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 125.359 α = 90 b = 50.05 β = 109.85 c = 136.705 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 2002-12-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID29 ESRF ID29
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 2.15 30 90 0.06 15 2.4 78453 2
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 2.15 2.23 90 0.23 2.3 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 ENTRIES 1DUZ, 7FAB, 2GFB, 2FB4 2.15 120 74477 3961 89.7 0.186 0.182 0.1926 0.248 0.2582 RANDOM 22.22
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] -0.08 -0.79 -0.38 -0.07
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.518 r_dihedral_angle_4_deg 14.169 r_dihedral_angle_3_deg 11.947 r_dihedral_angle_1_deg 4.482 r_scangle_it 2.908 r_scbond_it 2.036 r_angle_refined_deg 1.475 r_mcangle_it 1.374 r_mcbond_it 1.094 r_angle_other_deg 0.819
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.518 r_dihedral_angle_4_deg 14.169 r_dihedral_angle_3_deg 11.947 r_dihedral_angle_1_deg 4.482 r_scangle_it 2.908 r_scbond_it 2.036 r_angle_refined_deg 1.475 r_mcangle_it 1.374 r_mcbond_it 1.094 r_angle_other_deg 0.819 r_symmetry_vdw_other 0.233 r_symmetry_hbond_refined 0.218 r_symmetry_vdw_refined 0.211 r_nbd_refined 0.193 r_nbd_other 0.19 r_xyhbond_nbd_refined 0.157 r_chiral_restr 0.091 r_nbtor_refined 0.085 r_nbtor_other 0.085 r_bond_refined_d 0.012 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_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 12794 Nucleic Acid Atoms Solvent Atoms 653 Heterogen Atoms 24
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling AMoRE phasing