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Crystal structure of ACPA 1F2 in complex with CII-C-39-CIT
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5OCX
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 20mM Tris pH 7.4, 20mMNaCl, 20% (w/v) PEG 6000, 0.1M HEPES 7.0 pH 7.0, 0.01M zinc chloride.
Crystal Properties Matthews coefficient Solvent content 2.95 58.32
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 53.01 α = 90 b = 89.65 β = 90 c = 118.68 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 210 PIXEL DECTRIS PILATUS3 6M 2018-03-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.97662 Diamond I03
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 2.85 118.75 99.9 0.146 0.165 0.076 0.993 9.9 8.8 13893
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 2.85 3 0.501 0.569 0.267 0.914 8.7
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-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 5ocx 2.85 36.219 13539 638 98.137 0.213 0.2098 0.2762 0.249 39.044
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] -0.81 0.63 0.18
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.407 r_dihedral_angle_4_deg 17.154 r_dihedral_angle_3_deg 16.446 r_dihedral_angle_1_deg 8.123 r_lrange_it 2.348 r_lrange_other 2.345 r_angle_refined_deg 1.333 r_mcangle_it 1.143 r_mcangle_other 1.143 r_angle_other_deg 1.122
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.407 r_dihedral_angle_4_deg 17.154 r_dihedral_angle_3_deg 16.446 r_dihedral_angle_1_deg 8.123 r_lrange_it 2.348 r_lrange_other 2.345 r_angle_refined_deg 1.333 r_mcangle_it 1.143 r_mcangle_other 1.143 r_angle_other_deg 1.122 r_scangle_it 1.045 r_scangle_other 1.044 r_scbond_it 0.656 r_scbond_other 0.656 r_mcbond_it 0.646 r_mcbond_other 0.645 r_nbd_other 0.273 r_symmetry_nbd_refined 0.267 r_nbd_refined 0.185 r_symmetry_nbd_other 0.174 r_nbtor_refined 0.159 r_symmetry_xyhbond_nbd_refined 0.118 r_xyhbond_nbd_refined 0.117 r_symmetry_metal_ion_refined 0.112 r_metal_ion_refined 0.107 r_symmetry_nbtor_other 0.078 r_chiral_restr 0.044 r_bond_refined_d 0.004 r_gen_planes_refined 0.004 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3275 Nucleic Acid Atoms Solvent Atoms 33 Heterogen Atoms 64
Software Software Software Name Purpose REFMAC refinement REFMAC refinement Aimless data reduction XDS data reduction Coot model building