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Conformational Restraints and Flexibility of 14-Meric Peptides in Complex with HLA-B*3501
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1A1N PDB ENTRY 1A1N
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 293 PEG4000, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.52 51.26
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 50.828 α = 90 b = 81.663 β = 90 c = 109.798 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 mirrors 2002-12-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON MPG/DESY, HAMBURG BEAMLINE BW6 1.05 MPG/DESY, HAMBURG BW6
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 1.48 18.6 93.7 0.061 0.061 5.2 3.4 72270 72270 18.2
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 1.48 1.56 92 0.452 0.379 1.6 3.2 10253
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1A1N 1.48 18.6 72270 68581 3637 93.31 0.17979 0.17979 0.17825 0.1805 0.2082 RANDOM 17.43
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] -0.8 -0.74 1.54
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.279 r_dihedral_angle_4_deg 19.854 r_dihedral_angle_3_deg 13.198 r_dihedral_angle_1_deg 6.347 r_scangle_it 3.623 r_scbond_it 2.58 r_mcangle_it 1.591 r_angle_refined_deg 1.491 r_mcbond_it 1.459 r_angle_other_deg 0.819
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.279 r_dihedral_angle_4_deg 19.854 r_dihedral_angle_3_deg 13.198 r_dihedral_angle_1_deg 6.347 r_scangle_it 3.623 r_scbond_it 2.58 r_mcangle_it 1.591 r_angle_refined_deg 1.491 r_mcbond_it 1.459 r_angle_other_deg 0.819 r_symmetry_vdw_other 0.281 r_mcbond_other 0.273 r_symmetry_vdw_refined 0.221 r_nbd_refined 0.21 r_nbd_other 0.206 r_symmetry_hbond_refined 0.199 r_nbtor_refined 0.186 r_xyhbond_nbd_refined 0.174 r_chiral_restr 0.096 r_nbtor_other 0.085 r_bond_refined_d 0.013 r_gen_planes_refined 0.007 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3186 Nucleic Acid Atoms Solvent Atoms 562 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction CCP4 data scaling AMoRE phasing