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Ribonucleotide reductase Y730NO2Y modified R1 subunit of E. coli
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2X0X PDB ENTRY 2X0X
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 6 LITHIUM SULPHATE 1.5M, SODIUM CHLORIDE BUFFER PH 6.
Crystal Properties Matthews coefficient Solvent content 3.05 54
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 224.091 α = 90 b = 224.091 β = 90 c = 337.157 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 2009-01-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-2 ESRF ID14-2
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 2.8 67.27 100 0.14 16.17 9.71 79929 -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 2.8 2.82 100 0.64 3.35 8.41
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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 2X0X 2.8 169.031 2 79929 4011 99.982 0.181 0.1781 0.1774 0.2408 0.2362 RANDOM 36.914
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] 0.275 0.137 0.275 -0.412
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.475 r_dihedral_angle_3_deg 19.036 r_dihedral_angle_4_deg 18.925 r_dihedral_angle_1_deg 6.153 r_scangle_it 2.347 r_scbond_it 1.358 r_angle_refined_deg 1.327 r_mcangle_it 1.098 r_mcbond_it 0.607 r_nbtor_refined 0.31
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.475 r_dihedral_angle_3_deg 19.036 r_dihedral_angle_4_deg 18.925 r_dihedral_angle_1_deg 6.153 r_scangle_it 2.347 r_scbond_it 1.358 r_angle_refined_deg 1.327 r_mcangle_it 1.098 r_mcbond_it 0.607 r_nbtor_refined 0.31 r_symmetry_hbond_refined 0.299 r_nbd_refined 0.219 r_symmetry_vdw_refined 0.191 r_xyhbond_nbd_refined 0.159 r_chiral_restr 0.094 r_bond_refined_d 0.01 r_gen_planes_refined 0.004 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_refined 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 17835 Nucleic Acid Atoms Solvent Atoms 439 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction TRUNCATE data scaling REFMAC phasing