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Crystal structure of ACPA E4 in complex with CII-C-13-CIT
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4M1Q 4M1Q,3LMJ experimental model PDB 3LMJ 4M1Q,3LMJ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 20% (w/v) PEG3350, 0.2 M ammonium citrate dibasic
Crystal Properties Matthews coefficient Solvent content 1.82 32.06
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 38.716 α = 90 b = 99.602 β = 101.88 c = 51.877 γ = 90
Symmetry Space Group P 1 21 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 PILATUS 6M-F 2016-01-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I02 0.9795 Diamond I02
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.75 45.23 97.3 0.083 0.076 0.994 7.5 3.1 37660 15.2
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 1.75 1.78 90 0.584 0.539 0.606 1.3 2.7
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 (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 4M1Q,3LMJ 1.75 45.23 35680 1948 97.13 0.17812 0.17623 0.1843 0.21231 0.2188 RANDOM 23.114
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] 0.19 1.04 -2.03 1.3
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.371 r_dihedral_angle_4_deg 22.595 r_dihedral_angle_3_deg 11.687 r_dihedral_angle_1_deg 6.606 r_long_range_B_refined 4.627 r_long_range_B_other 4.627 r_scangle_other 2.443 r_mcangle_other 2.195 r_mcangle_it 2.193 r_angle_other_deg 1.581
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.371 r_dihedral_angle_4_deg 22.595 r_dihedral_angle_3_deg 11.687 r_dihedral_angle_1_deg 6.606 r_long_range_B_refined 4.627 r_long_range_B_other 4.627 r_scangle_other 2.443 r_mcangle_other 2.195 r_mcangle_it 2.193 r_angle_other_deg 1.581 r_scbond_it 1.532 r_scbond_other 1.531 r_angle_refined_deg 1.428 r_mcbond_it 1.337 r_mcbond_other 1.334 r_chiral_restr 0.08 r_bond_refined_d 0.009 r_gen_planes_refined 0.006 r_bond_other_d 0.002 r_gen_planes_other 0.001 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 3356 Nucleic Acid Atoms Solvent Atoms 400 Heterogen Atoms 4
Software Software Software Name Purpose REFMAC refinement xia2 data reduction Aimless data scaling PHASER phasing