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Ribonucleotide reductase class 1b holocomplex R1E,R2F from Salmonella typhimurium
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1PEM PDB ENTRY 1PEM
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7.5 1:1 MIX OF PROTEIN SOLUTION (8 MG/ML R1E, 4 MG/ML R2F, 1.5 MM DGTP, 1.5 MM ADP, 1.5 MM MGCL2 AND 1.5 MM HYDROXYUREA) AND RESERVOIR SOLUTION CONSISTING OF 100 MM NAHEPES PH 7.5 AND 1.8 M SODIUM FORMATE.
Crystal Properties Matthews coefficient Solvent content 3.79 66
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 270.372 α = 90 b = 270.372 β = 90 c = 270.372 γ = 90
Symmetry Space Group P 41 3 2
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 2004-04-23 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 4 40 99.8 0.15 13.5 15.1 29196 1
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 4 4.07 98.8 0.39 4 7.2
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 1PEM 3.99 182.57 27672 1484 99.7 0.265 0.262 0.2414 0.31 0.2938 RANDOM 65.31
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 5.546 r_scangle_it 1.07 r_angle_refined_deg 1.036 r_mcangle_it 0.724 r_scbond_it 0.574 r_mcbond_it 0.393 r_nbd_refined 0.216 r_symmetry_vdw_refined 0.187 r_symmetry_hbond_refined 0.176 r_xyhbond_nbd_refined 0.161
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 5.546 r_scangle_it 1.07 r_angle_refined_deg 1.036 r_mcangle_it 0.724 r_scbond_it 0.574 r_mcbond_it 0.393 r_nbd_refined 0.216 r_symmetry_vdw_refined 0.187 r_symmetry_hbond_refined 0.176 r_xyhbond_nbd_refined 0.161 r_metal_ion_refined 0.099 r_chiral_restr 0.071 r_bond_refined_d 0.007 r_gen_planes_refined 0.003 r_bond_other_d r_angle_other_deg r_dihedral_angle_2_deg r_dihedral_angle_3_deg r_dihedral_angle_4_deg r_gen_planes_other r_nbd_other r_nbtor_refined 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 15452 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 68
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling BEAST phasing