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Crystal structure of a cyclodipeptide synthase from Parcubacteria bacterium RAAC4_OD1_1, E174A mutant
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7QAE
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 2.27 M Ammonium Sulfate
0.1 M Sodium Acetate pH 5.17
Crystal Properties Matthews coefficient Solvent content 2.33 47.2
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 102.6 α = 90 b = 102.6 β = 90 c = 49.86 γ = 90
Symmetry Space Group P 42 21 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 PILATUS3 6M 2021-09-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I24 0.9999 Diamond I24
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 2.4 51.3 100 0.152 0.156 0.032 0.999 26.1 23.8 10919
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 2.4 2.46 99.9 0.711 0.727 0.147 0.959 23.6
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 THROUGHOUT 7QAE 2.4 45.884 1.34 10886 544 99.96 0.1953 0.1929 0.2027 0.24 0.2543 55.3753
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]
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1810 Nucleic Acid Atoms Solvent Atoms 24 Heterogen Atoms
Software Software Software Name Purpose PHENIX refinement Aimless data scaling PDB_EXTRACT data extraction PHASER phasing autoPROC data reduction