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Crystal structure of ACPA F3
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, 50mM NaCl, 0.2M Potassium thiocyanate, 2.2M Ammonium sulfate)
Crystal Properties Matthews coefficient Solvent content 2.78 55.75
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 130.886 α = 90 b = 130.886 β = 90 c = 61.026 γ = 90
Symmetry Space Group P 41 21 2
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 EIGER X 16M 2018-11-03 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 2.1 65.529 100 0.155 0.164 0.055 0.998 10.4 16.4 31556
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 2.1 2.16 1.463 1.554 0.522 0.855 16.8
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 2.1 65.529 31497 1551 99.978 0.2 0.1987 0.1988 0.2313 0.2312 42.449
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] -0.098 -0.098 0.196
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.19 r_dihedral_angle_4_deg 18.741 r_dihedral_angle_3_deg 14.32 r_dihedral_angle_1_deg 8.386 r_lrange_it 5.904 r_lrange_other 5.876 r_scangle_it 3.724 r_scangle_other 3.723 r_mcangle_it 2.516 r_mcangle_other 2.516
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.19 r_dihedral_angle_4_deg 18.741 r_dihedral_angle_3_deg 14.32 r_dihedral_angle_1_deg 8.386 r_lrange_it 5.904 r_lrange_other 5.876 r_scangle_it 3.724 r_scangle_other 3.723 r_mcangle_it 2.516 r_mcangle_other 2.516 r_scbond_it 2.338 r_scbond_other 2.337 r_angle_refined_deg 1.757 r_mcbond_it 1.695 r_mcbond_other 1.694 r_angle_other_deg 1.349 r_symmetry_nbd_refined 0.737 r_symmetry_xyhbond_nbd_refined 0.312 r_nbd_other 0.283 r_nbd_refined 0.253 r_symmetry_nbd_other 0.201 r_nbtor_refined 0.165 r_xyhbond_nbd_refined 0.146 r_symmetry_nbtor_other 0.082 r_chiral_restr 0.072 r_symmetry_xyhbond_nbd_other 0.019 r_bond_refined_d 0.011 r_gen_planes_refined 0.009 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3262 Nucleic Acid Atoms Solvent Atoms 189 Heterogen Atoms 11
Software Software Software Name Purpose REFMAC refinement REFMAC refinement Aimless data reduction XDS data reduction XDS data scaling