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Ribonucleotide Reductase NrdF from Escherichia coli Soaked with Ferrous Ions
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3N37
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7.6 25% PEG 4000, 0.1 M HEPES pH 7.6, 0.1 M lithium sulfate
Crystal Properties Matthews coefficient Solvent content 3.32 62.96
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 79.137 α = 90 b = 79.137 β = 90 c = 267.981 γ = 120
Symmetry Space Group P 65 2 2
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 2010-02-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-D 1.03324 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 1.9 68.53
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 3N37 1.9 68.53 38952 1956 97.3 0.197 0.196 0.2005 0.22 0.225 RANDOM 34.621
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] 0.98 0.49 0.98 -1.48
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.899 r_dihedral_angle_4_deg 20.556 r_dihedral_angle_3_deg 12.157 r_dihedral_angle_1_deg 4.618 r_scangle_it 2.998 r_scbond_it 1.723 r_angle_refined_deg 1.004 r_mcangle_it 0.911 r_mcbond_it 0.442 r_chiral_restr 0.07
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.899 r_dihedral_angle_4_deg 20.556 r_dihedral_angle_3_deg 12.157 r_dihedral_angle_1_deg 4.618 r_scangle_it 2.998 r_scbond_it 1.723 r_angle_refined_deg 1.004 r_mcangle_it 0.911 r_mcbond_it 0.442 r_chiral_restr 0.07 r_bond_refined_d 0.009 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2277 Nucleic Acid Atoms Solvent Atoms 154 Heterogen Atoms 2
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction