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Structural basis for degenerate recognition of HIV peptide variants by cytotoxic lymphocyte, variant SL9-3A
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2HLA PDB ENTRY 2HLA
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 6.5 293 15% polyethylene glycol 6000, 25mM MES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K, pH 6.50
Crystal Properties Matthews coefficient Solvent content 2.61 52.95
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 55.92 α = 90 b = 80.3 β = 116.29 c = 57.8 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 ADSC QUANTUM 4 2001-10-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X4A NSLS X4A
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 2.2 20 0.058 0.058 4039.3 20625 17.6
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) 2.2 85.5 0.096 0.096 1882
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 2HLA 2.2 11.94 20019 1019 86.2 0.19 0.19 0.1927 0.252 0.1923 RANDOM 23.2
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] 2.68 -2.65 -3.73 1.05
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 24.9 c_scangle_it 3.54 c_scbond_it 2.42 c_mcangle_it 2.08 c_mcbond_it 1.38 c_angle_deg 1.3 c_improper_angle_d 0.77 c_bond_d 0.008 c_bond_d_na c_bond_d_prot
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 24.9 c_scangle_it 3.54 c_scbond_it 2.42 c_mcangle_it 2.08 c_mcbond_it 1.38 c_angle_deg 1.3 c_improper_angle_d 0.77 c_bond_d 0.008 c_bond_d_na c_bond_d_prot c_angle_d c_angle_d_na c_angle_d_prot c_angle_deg_na c_angle_deg_prot c_dihedral_angle_d_na c_dihedral_angle_d_prot c_improper_angle_d_na c_improper_angle_d_prot
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3138 Nucleic Acid Atoms Solvent Atoms 356 Heterogen Atoms
Software Software Software Name Purpose CNS refinement DENZO data reduction SCALEPACK data scaling CNS phasing