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Structure of iron bound IbpS from Dickeya dadantii
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6FJL
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 292 20% PEG 3350
0.1M BisTrisPropane pH 8.5
0.2M NaNO3
Crystal Properties Matthews coefficient Solvent content 2.15 42.77
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 58.891 α = 73.251 b = 78.889 β = 74.741 c = 83.913 γ = 84.918
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 173 PIXEL DECTRIS PILATUS3 S 6M 2018-04-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 1.589539 ESRF ID23-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) 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 1.8 77.8 86.4 0.05938 0.06875 10 4 111675 22.1169963521
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.8 1.83 83.3 0.43 0.6 0.83 1.7 4
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 6FJL 1.80000342375 47.9914774494 1.9805155397 111650 5522 86.3395584426 0.156820705143 0.155029073565 0.1576 0.191143831402 0.1916 26.8548546431
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 12.9266239073 f_angle_d 1.11028455336 f_chiral_restr 0.0460748809093 f_bond_d 0.00783736213536 f_plane_restr 0.00563152447265
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 11004 Nucleic Acid Atoms Solvent Atoms 1129 Heterogen Atoms 16
Software Software Software Name Purpose PHENIX refinement XDS data reduction Aimless data scaling PHASER phasing