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Crystal structure of ACPA 3F3 in complex with cit-vimentin 59-74
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5OCX 5OCX(early model)
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 20mM Tris pH 7.5, 20mM NaCl, 0.2M ammonium chloride pH 6.3, (20%) w/v PEG 3350)
Crystal Properties Matthews coefficient Solvent content 3.03 59.4
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 53.379 α = 90 b = 82.094 β = 90 c = 135.613 γ = 90
Symmetry Space Group P 21 21 21
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 2018-11-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON MAX IV BEAMLINE BioMAX 0.91840 MAX IV BioMAX
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 52.334 99.5 0.122 0.14 0.067 0.996 9.9 8 40933
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2 2.05 0.936 1.069 0.511 0.676 8.2
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 5OCX(early model) 2 52.28 40902 2026 99.513 0.213 0.2105 0.2087 0.2534 0.2516 33.325
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] -0.926 -1.275 2.201
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.069 r_dihedral_angle_4_deg 21.968 r_dihedral_angle_3_deg 15.786 r_dihedral_angle_1_deg 8.14 r_lrange_it 7.168 r_lrange_other 7.065 r_scangle_it 2.821 r_scangle_other 2.821 r_angle_refined_deg 2.259 r_mcangle_it 2.051
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.069 r_dihedral_angle_4_deg 21.968 r_dihedral_angle_3_deg 15.786 r_dihedral_angle_1_deg 8.14 r_lrange_it 7.168 r_lrange_other 7.065 r_scangle_it 2.821 r_scangle_other 2.821 r_angle_refined_deg 2.259 r_mcangle_it 2.051 r_mcangle_other 2.051 r_scbond_it 1.842 r_scbond_other 1.838 r_angle_other_deg 1.472 r_mcbond_it 1.344 r_mcbond_other 1.344 r_nbd_other 0.272 r_symmetry_nbd_refined 0.253 r_nbd_refined 0.24 r_symmetry_nbd_other 0.211 r_symmetry_xyhbond_nbd_refined 0.205 r_xyhbond_nbd_refined 0.192 r_nbtor_refined 0.182 r_symmetry_nbtor_other 0.098 r_chiral_restr 0.093 r_bond_refined_d 0.018 r_gen_planes_refined 0.013 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3395 Nucleic Acid Atoms Solvent Atoms 303 Heterogen Atoms 64
Software Software Software Name Purpose REFMAC refinement REFMAC refinement XDS data reduction Coot model building XDS data scaling