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Crystal structure of ACPA E4 in complex with CII-C-48-CIT
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5OCY 5OCY(early model)
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 (20% (w/v) PEG 3350, 0.1M Bis-Tris propane, pH 6.5, 0.2M Potassium thiocyanate
Crystal Properties Matthews coefficient Solvent content 2.03 39.41
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 77.183 α = 90 b = 151.774 β = 90 c = 97.066 γ = 90
Symmetry Space Group C 2 2 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 293 PIXEL DECTRIS PILATUS 300K 2016-09-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.97625 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 2.45 97.07 99.9 0.05 0.056 0.025 0.998 22.4 9.2 21382
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 2.45 2.55 0.391 0.441 0.2 0.952 9.2
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 5OCY(early model) 2.45 75.887 21353 1129 99.972 0.225 0.2229 0.2234 0.2652 0.2644 60.539
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] -0.076 -0.462 0.539
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.153 r_dihedral_angle_4_deg 17.621 r_dihedral_angle_3_deg 16.652 r_dihedral_angle_1_deg 8.202 r_lrange_it 4.427 r_lrange_other 4.415 r_mcangle_it 2.627 r_mcangle_other 2.627 r_scangle_it 2.587 r_scangle_other 2.586
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.153 r_dihedral_angle_4_deg 17.621 r_dihedral_angle_3_deg 16.652 r_dihedral_angle_1_deg 8.202 r_lrange_it 4.427 r_lrange_other 4.415 r_mcangle_it 2.627 r_mcangle_other 2.627 r_scangle_it 2.587 r_scangle_other 2.586 r_scbond_it 1.701 r_scbond_other 1.701 r_angle_refined_deg 1.626 r_mcbond_it 1.618 r_mcbond_other 1.618 r_angle_other_deg 1.188 r_symmetry_xyhbond_nbd_refined 0.532 r_nbd_other 0.269 r_xyhbond_nbd_other 0.242 r_nbd_refined 0.192 r_symmetry_nbd_other 0.181 r_symmetry_nbd_refined 0.167 r_xyhbond_nbd_refined 0.166 r_nbtor_refined 0.163 r_symmetry_nbtor_other 0.083 r_chiral_restr 0.064 r_symmetry_xyhbond_nbd_other 0.039 r_bond_refined_d 0.008 r_gen_planes_refined 0.007 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3277 Nucleic Acid Atoms Solvent Atoms 45 Heterogen Atoms 39
Software Software Software Name Purpose REFMAC refinement REFMAC refinement Aimless data scaling XDS data reduction XDS data scaling