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Crystal Structure of the Class Ie Ribonucleotide Reductase Beta Subunit from Aerococcus urinae (in alternate conformation)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6EBO
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 298 15% (w/v) PEG 3350, 0.2 M calcium chloride, 0.1 M HEPBS pH 8.5, 10 mM sodium dithionite
Crystal Properties Matthews coefficient Solvent content 2.04 39.69
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 45.375 α = 109.4 b = 52.876 β = 106.41 c = 74.534 γ = 91.47
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD MARMOSAIC 300 mm CCD 2020-02-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-F 0.9787 APS 21-ID-F
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 1.55 50 96.6 0.021 0.024 0.012 21.2 4 86931
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 1.55 1.58 94.8 0.105 0.122 0.062 0.986 3.9
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) 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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 6EBO 1.55 33.82 82529 4402 96.43 0.1744 0.1732 0.1837 0.198 0.2054 RANDOM 12.004
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] 0.12 -0.04 0.01 -0.11 -0.03
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.813 r_dihedral_angle_3_deg 12.053 r_dihedral_angle_4_deg 9.019 r_dihedral_angle_1_deg 5.328 r_angle_other_deg 1.302 r_angle_refined_deg 1.133 r_chiral_restr 0.06 r_gen_planes_refined 0.004 r_bond_refined_d 0.003 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.813 r_dihedral_angle_3_deg 12.053 r_dihedral_angle_4_deg 9.019 r_dihedral_angle_1_deg 5.328 r_angle_other_deg 1.302 r_angle_refined_deg 1.133 r_chiral_restr 0.06 r_gen_planes_refined 0.004 r_bond_refined_d 0.003 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5119 Nucleic Acid Atoms Solvent Atoms 431 Heterogen Atoms 2
Software Software Software Name Purpose HKL-2000 data reduction HKL-2000 data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction