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Structure of human guanylylated RTCB in complex with Archease
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8BTT experimental model PDB 8BTX
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 291.15 protein: RTCB 160 uM, Archease 200 uM, 2 mM manganese chloride, 2 mM GTP
reservoir: 10% w/v PEG 8000, 0.1 M HEPES pH 7.5, 8% v/v ethylene glycol
drop: 200 nl protein + 200 nl reservoir
Crystal Properties Matthews coefficient Solvent content 2.42 49.24
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 99.09 α = 90 b = 125.547 β = 108.51 c = 125.733 γ = 90
Symmetry Space Group P 1 21 1
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 EIGER2 X 16M Toroidal mirror 2021-09-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 0.9737 ESRF ID23-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 2.2 119.23 99.3 0.11 0.045 0.998 9.2 7 145859 44.78
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.2 2.24 95.2 1.16 0.495 0.86 1.1 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 D_1292120363 2.2 75.23 1.34 145538 7183 99.15 0.1945 0.1933 0.1914 0.2176 0.2159 65.24
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 12.9423 f_angle_d 0.4961 f_chiral_restr 0.0429 f_plane_restr 0.004 f_bond_d 0.0022
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 20965 Nucleic Acid Atoms Solvent Atoms 643 Heterogen Atoms 120
Software Software Software Name Purpose PHENIX refinement XDS data reduction Aimless data scaling PHASER phasing