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Crystal structure of class Ie ribonucleotide reductase R2 subunit with post-translational modification of Y150 into a DOPA from Gardnerella vaginalis
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other The structure was originally solved by MR with a SwissModel PDB. This structure was solved using a PDB from a previous experiment.
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 293 Morpheus G4 condition (0.1 M Carboxylic acids, 0.1 M Buffer System 1 pH 6.5, 37.5% v/v Precipitant Mix 4) + 4% tert-butanol
Crystal Properties Matthews coefficient Solvent content 4.09 69.9
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 173.71 α = 90 b = 173.71 β = 90 c = 157.89 γ = 120
Symmetry Space Group P 31 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 EIGER X 16M 2019-11-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON MAX IV BEAMLINE BioMAX 0.97622 MAX IV BioMAX
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 1.9 49.68 99.63 0.1316 0.1357 0.03279 0.999 13.2 16.9 215066 45.56
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 1.9 1.968 96.6 4.584 4.761 1.275 0.271 0.4 13.7
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 1.9 49.68 1.33 214297 1839 99.64 0.1712 0.171 0.1715 0.1892 0.1898 51.91
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 13.0992 f_angle_d 0.7585 f_chiral_restr 0.0466 f_plane_restr 0.0082 f_bond_d 0.0069
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 10562 Nucleic Acid Atoms Solvent Atoms 754 Heterogen Atoms
Software Software Software Name Purpose PHENIX refinement XDS data reduction XDS data scaling PHASER phasing