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Crystal structure of DR11 presenting the gag293 epitope
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4MDO
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 295 PEG 3350, Tris pH 8.5, Ethylene glycol
Crystal Properties Matthews coefficient Solvent content 2.73 55
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 65.746 α = 90 b = 65.746 β = 90 c = 222.514 γ = 120
Symmetry Space Group P 31 1 2
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 315r 2016-03-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON AUSTRALIAN SYNCHROTRON BEAMLINE MX2 0.984 Australian Synchrotron MX2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Rpim I (All) 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 2.45 45.16 100 0.052 14.9 10.9 20598 58.05
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.45 2.55 0.435
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 4MDO 2.45 45.16 20598 1059 99.48 0.225 0.2236 0.2242 0.2529 0.2567 RANDOM 44.09
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] -0.6871 -0.6871 1.3741
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 17.43 t_omega_torsion 2.73 t_angle_deg 0.98 t_bond_d 0.007 t_dihedral_angle_d t_incorr_chiral_ct t_pseud_angle t_trig_c_planes t_gen_planes t_it
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 17.43 t_omega_torsion 2.73 t_angle_deg 0.98 t_bond_d 0.007 t_dihedral_angle_d t_incorr_chiral_ct t_pseud_angle t_trig_c_planes t_gen_planes t_it t_nbd t_improper_torsion t_chiral_improper_torsion t_sum_occupancies t_utility_distance t_utility_angle t_utility_torsion t_ideal_dist_contact
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3186 Nucleic Acid Atoms Solvent Atoms 185 Heterogen Atoms 92
Software Software Software Name Purpose BUSTER refinement XDS data reduction Aimless data scaling