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DeAMPylation complex of monomeric FICD and AMPylated BiP (state 2)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5O4P 5O4P, 6I7L experimental model PDB 6I7L 5O4P, 6I7L
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8 298 0.1 M Tris pH 8.0
25% PEG 400
Crystal Properties Matthews coefficient Solvent content 2.72 54.74
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 95 α = 90 b = 103.89 β = 90 c = 104.79 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 PILATUS 6M-F 2019-07-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 0.9159 Diamond I04-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.87 52.4 100 0.087 0.999 11.9 6.6 86247
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.87 1.92 100 1.793 0.536 1 6.9
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 5O4P, 6I7L 1.87 52.4 81979 4190 99.96 0.2021 0.2008 0.2061 0.2278 0.2365 RANDOM 37.354
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] -1.58 -1.09 2.68
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.734 r_dihedral_angle_4_deg 13.697 r_dihedral_angle_3_deg 12.621 r_dihedral_angle_1_deg 5.789 r_angle_refined_deg 1.199 r_angle_other_deg 1.151 r_chiral_restr 0.048 r_gen_planes_refined 0.004 r_bond_refined_d 0.003 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.734 r_dihedral_angle_4_deg 13.697 r_dihedral_angle_3_deg 12.621 r_dihedral_angle_1_deg 5.789 r_angle_refined_deg 1.199 r_angle_other_deg 1.151 r_chiral_restr 0.048 r_gen_planes_refined 0.004 r_bond_refined_d 0.003 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6766 Nucleic Acid Atoms Solvent Atoms 590 Heterogen Atoms 84
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction xia2 data reduction Aimless data scaling PHASER phasing