☰ Navigation Tabs
Crystal Structure of N-terminal Domain of Fic Family Protein from Bordetella bronchiseptica
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 292 Protein: 4.5 mg/ml, 0.5M Sodium chloride, 0.01M Tris pH 8.3, 5% Gly, 2mM GDP, 2mM Magnesium chloride;
Screen: Classics II (C6), 0.8M Sodium/Potassium tartrate, 0.1M Bis-Tris pH 8.5, 0.5% (w/v) PEG 5000 MME;
Cryo: 20% Glycerole in screen solution.
Crystal Properties Matthews coefficient Solvent content 5.14 76.1
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 149.971 α = 90 b = 149.971 β = 90 c = 371.921 γ = 120
Symmetry Space Group P 65 2 2
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 EIGER X 9M 2021-06-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-D 0.9789 APS 21-ID-D
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 2.95 30 100 0.199 0.199 0.05 0.999 16.8 16.5 53143 -3 78.7
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.95 3 100 0.528 0.593 1.5 17.2
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 2.95 29.91 50134 2699 99.81 0.1791 0.1776 0.1774 0.2069 0.2034 RANDOM 78.553
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] 0.79 0.4 0.79 -2.57
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 20.536 r_dihedral_angle_4_deg 9.582 r_dihedral_angle_3_deg 9.409 r_dihedral_angle_1_deg 1.617 r_angle_refined_deg 1.375 r_angle_other_deg 0.37 r_chiral_restr 0.068 r_gen_planes_refined 0.054 r_gen_planes_other 0.046 r_bond_refined_d 0.004
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 20.536 r_dihedral_angle_4_deg 9.582 r_dihedral_angle_3_deg 9.409 r_dihedral_angle_1_deg 1.617 r_angle_refined_deg 1.375 r_angle_other_deg 0.37 r_chiral_restr 0.068 r_gen_planes_refined 0.054 r_gen_planes_other 0.046 r_bond_refined_d 0.004 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6000 Nucleic Acid Atoms Solvent Atoms 115 Heterogen Atoms 137
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction HKL-3000 data reduction HKL-3000 data scaling PHASER phasing