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Crystal Structure of the Class Ie Ribonucleotide Reductase Beta-NrdI complex from Aerococcus urinae in Reduced Hydroquinone Form
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 19% (w/v) PEG 3350, 0.2 M calcium chloride, 0.1 M Tris pH 8.5, 10 mM sodium dithionite
Crystal Properties Matthews coefficient Solvent content 2.5 50.87
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 78.385 α = 90 b = 105.012 β = 100.58 c = 138.128 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 EIGER X 16M 2019-04-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 23-ID-B 1.0332 APS 23-ID-B
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 2.4 50 98.3 0.086 0.094 0.038 7.2 5.9 84812
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 2.44 83.4 0.772 0.887 0.426 0.573 3.6
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 2.4 49.69 74743 3983 91.17 0.2005 0.1983 0.2041 0.2408 0.2425 RANDOM 38.612
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] -0.38 0.1 0.35 -0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.064 r_dihedral_angle_3_deg 15.347 r_dihedral_angle_4_deg 13.993 r_dihedral_angle_1_deg 5.659 r_angle_refined_deg 1.177 r_angle_other_deg 1.098 r_chiral_restr 0.046 r_bond_refined_d 0.003 r_gen_planes_refined 0.003 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.064 r_dihedral_angle_3_deg 15.347 r_dihedral_angle_4_deg 13.993 r_dihedral_angle_1_deg 5.659 r_angle_refined_deg 1.177 r_angle_other_deg 1.098 r_chiral_restr 0.046 r_bond_refined_d 0.003 r_gen_planes_refined 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 14291 Nucleic Acid Atoms Solvent Atoms 206 Heterogen Atoms 142
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHASER phasing PDB_EXTRACT data extraction