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Crystal Structure of VpsR display novel dimeric architecture and c-di-GMP binding: mechanistic implications in oligomerization, ATPase activity and DNA binding.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1NY5
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 AMS(0.8M) Bicene pH 8.8
Crystal Properties Matthews coefficient Solvent content 3.55 61.45
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 118.639 α = 90 b = 118.639 β = 90 c = 78.255 γ = 120
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 2021-01-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 0.97242 ESRF ID23-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) 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 3.2 47.34 99.8 0.087 0.105 0.057 0.812 9.1 3.2 65219
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3.2 3.31 99.4 1.54 1.851 1.002 0.329 0.6 3
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 1NY5 3.2 47.273 0.1 20381 3615 90.29 0.2191 0.214 0.2303 0.2643 0.2326
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 17.041 f_angle_d 1.05 f_chiral_restr 0.038 f_bond_d 0.004 f_plane_restr 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5887 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 64
Software Software Software Name Purpose PHENIX refinement XDS data reduction Aimless data scaling PHASER phasing