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Ribonucleotide reductase Y730NO2Y and Y731F 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 3.18 54
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 223.893 α = 90 b = 223.893 β = 90 c = 336.73 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 QUANTUM Q4R 2009-04-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-1 ESRF ID14-1
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 3.1 93.25 98.9 0.13 11.85 4.53 58056 -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 3.1 3.13 98.6 0.48 2.18 4.31
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 2X0X 3.1 169.031 2 58056 2938 98.572 0.169 0.1652 0.2336 0.1927 RANDOM 43.8
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] -0.021 -0.01 -0.021 0.031
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.104 r_dihedral_angle_3_deg 20.674 r_dihedral_angle_4_deg 18.326 r_dihedral_angle_1_deg 6.534 r_scangle_it 2.182 r_angle_refined_deg 1.441 r_scbond_it 1.244 r_mcangle_it 1.044 r_mcbond_it 0.565 r_nbtor_refined 0.315
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.104 r_dihedral_angle_3_deg 20.674 r_dihedral_angle_4_deg 18.326 r_dihedral_angle_1_deg 6.534 r_scangle_it 2.182 r_angle_refined_deg 1.441 r_scbond_it 1.244 r_mcangle_it 1.044 r_mcbond_it 0.565 r_nbtor_refined 0.315 r_symmetry_hbond_refined 0.265 r_nbd_refined 0.237 r_symmetry_vdw_refined 0.2 r_xyhbond_nbd_refined 0.169 r_chiral_restr 0.1 r_bond_refined_d 0.012 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 17688 Nucleic Acid Atoms Solvent Atoms 532 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction TRUNCATE data scaling