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LOV-activated diguanylate cyclase, dark-state structure
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold AF-A0A2S5LZS0-F1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 293 0.1 M Sodium formate, 0.1 M Ammonium acetate, 0.1 M Sodium citrate tribasic dihydrate, 0.1 M Potassium sodium tartrate tetrahydrate, 0.1 M Sodium oxamate, 0.1 M Sodium HEPES; MOPS (acid), pH 7.5, 20% v/v Glycerol; 10% w/v PEG 4000
Crystal Properties Matthews coefficient Solvent content 2.02 39.1
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 56.35 α = 90 b = 56.35 β = 90 c = 318.04 γ = 120
Symmetry Space Group P 61 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 16M 2021-11-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, DESY BEAMLINE P11 1.03312 PETRA III, DESY P11
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Rrim 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 2.5 50 99.9 0.06 1 27.21 4.5 11310 80.05
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.5 2.6 99.8 0.82 0.993 4.39 5.36
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 2.5 48.8 1.34 11153 558 98.51 0.2569 0.2547 0.2705 0.2978 0.3127 114.09
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 10.0939 f_angle_d 0.3933 f_chiral_restr 0.0382 f_plane_restr 0.0023 f_bond_d 0.0015
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2433 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 41
Software Software Software Name Purpose PHENIX model building PHENIX refinement XDS data reduction XSCALE data scaling PHASER phasing