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Ribonucleotide Reductase Protein R1E from Salmonella typhimurium
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1RLR poly-alanin model of ribonucleotide reductase protein R1 from E.coli
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.2 288 sodium malonate, magnesium chloride, DTT, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 288K
Crystal Properties Matthews coefficient Solvent content 4.41 72.09
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 99.144 α = 90 b = 99.144 β = 90 c = 289.544 γ = 90
Symmetry Space Group P 43 21 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 QUANTUM 4 2002-07-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-1 0.9393 ESRF ID14-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 40 99.1 0.079 0.079 18.3 7.94 36371 36371
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 2.8 2.85 99.1 0.286 0.286 5.5
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 poly-alanin model of ribonucleotide reductase protein R1 from E.coli 2.8 40 34536 34536 1815 99.26 0.2166 0.2166 0.21507 0.2162 0.2464 0.2442 RANDOM 48.589
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] -0.01 -0.01 0.03
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 16.961 r_scangle_it 4.397 r_dihedral_angle_1_deg 3.373 r_scbond_it 2.564 r_angle_refined_deg 1.931 r_mcangle_it 1.92 r_mcbond_it 1.013 r_angle_other_deg 0.926 r_nbd_refined 0.271 r_symmetry_vdw_other 0.234
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 16.961 r_scangle_it 4.397 r_dihedral_angle_1_deg 3.373 r_scbond_it 2.564 r_angle_refined_deg 1.931 r_mcangle_it 1.92 r_mcbond_it 1.013 r_angle_other_deg 0.926 r_nbd_refined 0.271 r_symmetry_vdw_other 0.234 r_nbd_other 0.227 r_symmetry_vdw_refined 0.174 r_xyhbond_nbd_refined 0.138 r_chiral_restr 0.108 r_symmetry_hbond_refined 0.093 r_xyhbond_nbd_other 0.083 r_bond_refined_d 0.023 r_gen_planes_refined 0.008 r_gen_planes_other 0.003 r_bond_other_d 0.001 r_nbtor_other r_symmetry_hbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5423 Nucleic Acid Atoms Solvent Atoms 11 Heterogen Atoms 30
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling AMoRE phasing