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HLA-B*2709 BOUND TO NONA-PEPTIDE M9
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1JGE PDB ENTRY 1JGE (HLA-B*2705:m9), with Asp-A116 truncated to Ala
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 9 291 PEG 8000, Bicine, NaCl, glycerol as cryo protectant, pH 9.00, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 2.6 53
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 50.845 α = 90 b = 82.484 β = 90 c = 110.708 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 ADSC QUANTUM 4 2001-06-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-4 0.9393 ESRF ID14-4
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 1.09 19.1 96.7 0.091 12.8 4.7 187545 187545 5.8
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 1.09 1.12 96.8 0.376 2.9 2.9 12377
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 (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1JGE (HLA-B*2705:m9), with Asp-A116 truncated to Ala 1.09 19.1 181945 181945 5660 96.8 0.12349 0.12349 0.12275 0.1279 0.14755 0.1507 RANDOM 11.517
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] -0.21 -0.38 0.59
RMS Deviations Key Refinement Restraint Deviation p_scangle_it 3.906 p_scbond_it 2.91 p_mcangle_it 2.678 p_angle_deg 2.262 p_mcbond_it 1.961 p_bond_d 0.022
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3155 Nucleic Acid Atoms Solvent Atoms 959 Heterogen Atoms 12
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling AMoRE phasing REFMAC refinement