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Crystal Structure of the Class Ie Ribonucleotide Reductase Beta Subunit from Aerococcus urinae in Unactivated Form
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1KGN
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 298 16% (w/v) PEG 4000, 0.3 M calcium chloride, 0.1 M Tris pH 8.5
Crystal Properties Matthews coefficient Solvent content 2.24 45.12
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 79.847 α = 90 b = 109.074 β = 90.04 c = 83.728 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 CCD RAYONIX MX-300 2018-03-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-F 0.97872 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 1.58 50 99.3 0.111 0.12 0.044 7.9 7.3 194118
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 1.58 1.61 88.8 0.649 0.718 0.3 0.759 5.5
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 1KGN 1.58 39.67 178488 9388 96.49 0.1622 0.1617 0.1872 0.1722 0.1994 RANDOM 13.584
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] -1.05 1.6 1.56 -0.5
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.629 r_dihedral_angle_3_deg 12.42 r_dihedral_angle_4_deg 9.7 r_dihedral_angle_1_deg 5.078 r_angle_refined_deg 1.062 r_angle_other_deg 0.888 r_chiral_restr 0.061 r_bond_refined_d 0.007 r_gen_planes_refined 0.004 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.629 r_dihedral_angle_3_deg 12.42 r_dihedral_angle_4_deg 9.7 r_dihedral_angle_1_deg 5.078 r_angle_refined_deg 1.062 r_angle_other_deg 0.888 r_chiral_restr 0.061 r_bond_refined_d 0.007 r_gen_planes_refined 0.004 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 10024 Nucleic Acid Atoms Solvent Atoms 720 Heterogen Atoms 30
Software Software Software Name Purpose HKL-2000 data reduction HKL-2000 data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction