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Crystal structure of chloroplast FtsY from Arabidopsis thaliana in complex with the alarmone ppGpp
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2OG2
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 293 200 mM Tris-HCl pH 8.5; 25% PEG1000
Crystal Properties Matthews coefficient Solvent content 2.11 41.62
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 138.28 α = 90 b = 37.07 β = 110.628 c = 59.82 γ = 90
Symmetry Space Group C 1 2 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 PILATUS 6M 2022-06-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID30B 0.976253 ESRF ID30B
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 1.99 35.64 99.63 0.1176 0.1284 0.05077 0.996 14.86 6.3 19770 35.56
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 1.99 2.061 99.5 0.5475 0.606 0.2551 0.917 2.95 5.5
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 1.99 35.64 1.36 19757 984 99.65 0.2221 0.2193 0.2189 0.2758 0.273 42.64
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 9.5388 f_angle_d 1.2577 f_chiral_restr 0.0655 f_plane_restr 0.0096 f_bond_d 0.0092
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2224 Nucleic Acid Atoms Solvent Atoms 102 Heterogen Atoms 37
Software Software Software Name Purpose PHENIX refinement Coot model building XDS data reduction XSCALE data scaling PHENIX phasing