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Ribonucleotide reductase Y122NO2Y modified R2 subunit of E. coli
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1AV8 PDB ENTRY 1AV8
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 7.9 VAPOR DIFFUSION USING 90% OF SATURATED NACL, PH 7.9
Crystal Properties Matthews coefficient Solvent content 3.41 59.8
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 137.103 α = 90 b = 137.103 β = 90 c = 108.973 γ = 120
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 ADSC CCD 2010-01-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID29 ESRF ID29
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 2.2 80.29 99.9 0.12 9.59 3.68 59034 -3.7
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.2 2.22 99.8 0.54 2 3.62
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 PDB ENTRY 1AV8 2.2 118.68 56017 2985 99.91 0.1934 0.19182 0.1908 0.22352 0.2226 RANDOM 31.856
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] 1.04 0.52 1.04 -1.56
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.779 r_dihedral_angle_3_deg 17.304 r_dihedral_angle_4_deg 16.527 r_dihedral_angle_1_deg 4.626 r_scangle_it 1.793 r_angle_refined_deg 1.123 r_scbond_it 1.08 r_mcangle_it 0.856 r_mcbond_it 0.479 r_nbtor_refined 0.296
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.779 r_dihedral_angle_3_deg 17.304 r_dihedral_angle_4_deg 16.527 r_dihedral_angle_1_deg 4.626 r_scangle_it 1.793 r_angle_refined_deg 1.123 r_scbond_it 1.08 r_mcangle_it 0.856 r_mcbond_it 0.479 r_nbtor_refined 0.296 r_nbd_refined 0.193 r_symmetry_vdw_refined 0.147 r_xyhbond_nbd_refined 0.14 r_metal_ion_refined 0.14 r_symmetry_hbond_refined 0.105 r_chiral_restr 0.081 r_bond_refined_d 0.008 r_gen_planes_refined 0.003 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5584 Nucleic Acid Atoms Solvent Atoms 371 Heterogen Atoms 6
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling REFMAC phasing