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Crystal structure of non-phosphorylated form 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 6.5 298 19% PEG3350, 0.1 M Bis-Tris propane, 0.1 M sodium tartrate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.57 52.17
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 56.4 α = 90 b = 79.3 β = 115.5 c = 56.8 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 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 2.101 19.891 99.3 0.088 25.24 11.4 26307 -3 20.796
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 2.101 2.4 98.8 0.24 11.35
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 2.101 19.89 26305 1272 99.79 0.1901 0.1878 0.1886 0.2367 0.2378 RANDOM 14.1871
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] -0.01 0.01 -0.01 0.03
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.798 r_dihedral_angle_4_deg 16.555 r_dihedral_angle_3_deg 14.844 r_dihedral_angle_1_deg 6.209 r_scangle_it 2.943 r_scbond_it 1.73 r_angle_refined_deg 1.135 r_mcangle_it 1.086 r_mcbond_it 0.551 r_chiral_restr 0.08
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.798 r_dihedral_angle_4_deg 16.555 r_dihedral_angle_3_deg 14.844 r_dihedral_angle_1_deg 6.209 r_scangle_it 2.943 r_scbond_it 1.73 r_angle_refined_deg 1.135 r_mcangle_it 1.086 r_mcbond_it 0.551 r_chiral_restr 0.08 r_bond_refined_d 0.01 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3144 Nucleic Acid Atoms Solvent Atoms 265 Heterogen Atoms 13
Software Software Software Name Purpose d*TREK data scaling XSCALE data scaling REFMAC refinement PDB_EXTRACT data extraction CrystalClear data collection MOLREP phasing