☰ Navigation Tabs
Crystal structure of AMPD2 phosphopeptide bound to HLA-A2
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3BH9 PDB ENTRY 3BH9
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 298 12% PEG3350, 8% tacsimate, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.64 53.4
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 118 α = 90 b = 55.2 β = 104.9 c = 75.1 γ = 90
Symmetry Space Group C 1 2 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 RIGAKU SATURN 944 2010-09-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU 1.5417
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 1.703 20.052 91.9 0.034 33.95 7.2 46573 -3 28.19
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 1.703 1.9 75.4 0.328 4.68
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 3BH9 1.703 20.052 46573 2317 90.88 0.2091 0.208 0.2098 0.2318 0.2344 RANDOM 21.6785
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 -0.06 -0.13 0.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.72 r_dihedral_angle_4_deg 16.169 r_dihedral_angle_3_deg 13.152 r_dihedral_angle_1_deg 5.568 r_scangle_it 2.472 r_scbond_it 1.462 r_angle_refined_deg 1.111 r_mcangle_it 1.005 r_mcbond_it 0.525 r_chiral_restr 0.085
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.72 r_dihedral_angle_4_deg 16.169 r_dihedral_angle_3_deg 13.152 r_dihedral_angle_1_deg 5.568 r_scangle_it 2.472 r_scbond_it 1.462 r_angle_refined_deg 1.111 r_mcangle_it 1.005 r_mcbond_it 0.525 r_chiral_restr 0.085 r_bond_refined_d 0.008 r_gen_planes_refined 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3146 Nucleic Acid Atoms Solvent Atoms 390 Heterogen Atoms 16
Software Software Software Name Purpose d*TREK data scaling XSCALE data scaling MOLREP phasing REFMAC refinement PDB_EXTRACT data extraction CrystalClear data collection