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DeAMPylation complex of monomeric FICD and AMPylated BiP (state 1)
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 6.5 298 0.1 M MES pH 6.5
10% PEG 4000
0.2 M NaCl
Crystal Properties Matthews coefficient Solvent content 2.7 54.52
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 95.371 α = 90 b = 104.076 β = 90 c = 105.629 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 1.7 105.63 99.8 0.085 0.992 10.3 6.6 115633
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 1.7 1.73 99.3 1.299 0.585 1.2 6.5
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 1.7 74.25 109568 5973 99.65 0.1961 0.1948 0.2022 0.2208 0.2251 RANDOM 28.996
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] -0.6 -0.89 1.49
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.934 r_dihedral_angle_4_deg 12.666 r_dihedral_angle_3_deg 12.624 r_dihedral_angle_1_deg 5.623 r_angle_other_deg 1.178 r_angle_refined_deg 1.171 r_chiral_restr 0.048 r_bond_refined_d 0.003 r_gen_planes_refined 0.003 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.934 r_dihedral_angle_4_deg 12.666 r_dihedral_angle_3_deg 12.624 r_dihedral_angle_1_deg 5.623 r_angle_other_deg 1.178 r_angle_refined_deg 1.171 r_chiral_restr 0.048 r_bond_refined_d 0.003 r_gen_planes_refined 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 6667 Nucleic Acid Atoms Solvent Atoms 960 Heterogen Atoms 35
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction DIALS data reduction Aimless data scaling PHASER phasing