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Ro60 peptide bound to human HLA-DR3
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1A6A
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 298 0.2M of Sodium Malon salt, 20%w/v PEG3350
Crystal Properties Matthews coefficient Solvent content 3.11 60.41
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 110.621 α = 90 b = 96.843 β = 98.6 c = 102.595 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 PIXEL DECTRIS EIGER X 16M 2023-10-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON AUSTRALIAN SYNCHROTRON BEAMLINE MX2 0.95373 Australian Synchrotron MX2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) 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 2.59 48.42 99.3 0.193 0.218 0.1 0.988 7.3 0.05 33125 45.49
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.59 2.71 97.7 1.392 0.712 0.571
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 2.87 45.43 23313 1156 99.34 0.22883 0.22671 0.2403 0.27212 0.2872 RANDOM 42.986
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] 2.55 -0.92 -3.03 0.73
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 17.028 r_dihedral_angle_2_deg 8.634 r_dihedral_angle_1_deg 8.437 r_long_range_B_other 6.839 r_long_range_B_refined 6.838 r_mcangle_it 4.793 r_mcangle_other 4.792 r_scangle_other 4.593 r_mcbond_it 2.99 r_mcbond_other 2.988
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 17.028 r_dihedral_angle_2_deg 8.634 r_dihedral_angle_1_deg 8.437 r_long_range_B_other 6.839 r_long_range_B_refined 6.838 r_mcangle_it 4.793 r_mcangle_other 4.792 r_scangle_other 4.593 r_mcbond_it 2.99 r_mcbond_other 2.988 r_scbond_it 2.913 r_scbond_other 2.913 r_angle_refined_deg 1.459 r_angle_other_deg 0.97 r_chiral_restr 0.065 r_bond_other_d 0.043 r_bond_refined_d 0.008 r_gen_planes_refined 0.006 r_gen_planes_other 0.001 r_dihedral_angle_4_deg 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 6126 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement pointless data scaling PHASER phasing XDS data reduction Aimless data scaling