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Ribonucleotide Reductase Dimanganese(II)-NrdF from Escherichia coli in Complex with Reduced NrdI
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3N39
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7 20% PEG 3000, 0.1 M HEPES pH 7, 0.2 M lithium sulfate, 3 mM sodium dithionite
Crystal Properties Matthews coefficient Solvent content 2.27 45.89
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 74.863 α = 90 b = 90.678 β = 90 c = 143.837 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 113 CCD MARMOSAIC 225 mm CCD 2010-03-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-D 1.0781 APS 21-ID-D
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 1.99 29.58
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 3N39 1.99 29.58 67011 3406 99.27 0.204 0.203 0.2081 0.227 0.2303 RANDOM 35.252
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] 0.16 -0.01 -0.15
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.595 r_dihedral_angle_4_deg 17.388 r_dihedral_angle_3_deg 14.46 r_dihedral_angle_1_deg 4.9 r_scangle_it 2.381 r_scbond_it 1.433 r_angle_refined_deg 1.053 r_mcangle_it 0.904 r_mcbond_it 0.46 r_chiral_restr 0.079
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.595 r_dihedral_angle_4_deg 17.388 r_dihedral_angle_3_deg 14.46 r_dihedral_angle_1_deg 4.9 r_scangle_it 2.381 r_scbond_it 1.433 r_angle_refined_deg 1.053 r_mcangle_it 0.904 r_mcbond_it 0.46 r_chiral_restr 0.079 r_bond_refined_d 0.009 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6619 Nucleic Acid Atoms Solvent Atoms 280 Heterogen Atoms 66
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction