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crystal structure of antigen-ERAP1 domain complex
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3RJO
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 277 100 mM Tris, pH 8.5 and 16% PEG8000
Crystal Properties Matthews coefficient Solvent content 2.75 55.28
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 64.26 α = 90 b = 66.85 β = 110.16 c = 66.5 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 210 2014-06-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X29A 1.1 NSLS X29A
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 2.8 62.43 77 6.6 2.4 10114
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 2.8 2.95 81.3 0.335 2.3 2.3
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 3RJO 2.8 62.43 9400 500 75.14 0.20987 0.2067 0.2204 0.2689 0.281 RANDOM 28.119
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] 0.22 0.12 -0.48 0.14
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.657 r_dihedral_angle_4_deg 19.68 r_dihedral_angle_3_deg 17.236 r_dihedral_angle_1_deg 7.009 r_long_range_B_refined 4.26 r_long_range_B_other 4.259 r_mcangle_it 2.773 r_mcangle_other 2.772 r_scangle_other 2.697 r_mcbond_it 1.623
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.657 r_dihedral_angle_4_deg 19.68 r_dihedral_angle_3_deg 17.236 r_dihedral_angle_1_deg 7.009 r_long_range_B_refined 4.26 r_long_range_B_other 4.259 r_mcangle_it 2.773 r_mcangle_other 2.772 r_scangle_other 2.697 r_mcbond_it 1.623 r_mcbond_other 1.622 r_angle_refined_deg 1.61 r_scbond_it 1.573 r_scbond_other 1.569 r_angle_other_deg 1.022 r_chiral_restr 0.085 r_bond_refined_d 0.012 r_gen_planes_refined 0.006 r_bond_other_d 0.002 r_gen_planes_other 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3328 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement iMOSFLM data reduction xia2 data reduction PHASER phasing