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Structural basis for degenerate recognition of HIV peptide variants by cytotoxic lymphocyte, variant SL9-6I
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 VAPOR DIFFUSION, HANGING DROP 6.5 293 PEG, MES, pH 6.50, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.63 53.25
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 56.46 α = 90 b = 80.08 β = 116.38 c = 57.96 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) 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 20 21603 18.9
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 (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 11.93 22004 22004 1105 93.8 0.197 0.197 0.1992 0.247 0.1956 RANDOM 28.7
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] 6.21 -4.8 -8.56 2.35
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 24.8 c_scangle_it 3.61 c_scbond_it 2.41 c_mcangle_it 2.15 c_mcbond_it 1.4 c_angle_deg 1.2 c_improper_angle_d 0.75 c_bond_d 0.008 c_bond_d_na c_bond_d_prot
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 24.8 c_scangle_it 3.61 c_scbond_it 2.41 c_mcangle_it 2.15 c_mcbond_it 1.4 c_angle_deg 1.2 c_improper_angle_d 0.75 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 3146 Nucleic Acid Atoms Solvent Atoms 288 Heterogen Atoms
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling CNS refinement CNS phasing