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Structures of Yeast Ribonucleotide Reductase I
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other native structure
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 EVAPORATION 6.5 298 PEG 3350, sodium acetate, ammonium sulfate, pH 6.5, EVAPORATION, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.04 37.3
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 107.526 α = 90 b = 117.389 β = 90 c = 64.831 γ = 90
Symmetry Space Group P 21 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 IMAGE PLATE RIGAKU RAXIS IV 2005-04-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RUH3R 1.5418
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 2.4 50 98.1 0.071 0.071 11.3 4.7 32305 32305
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) 2.4 2.49 98.8 0.42 0.42 2.9 4.4 3193
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 native structure 2.4 50 29018 3244 98.17 0.2104 0.20431 0.2036 0.26587 0.2635 RANDOM 43.66
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] -2.6 -1.65 4.25
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.902 r_dihedral_angle_4_deg 21.106 r_dihedral_angle_3_deg 19.382 r_dihedral_angle_1_deg 6.768 r_scangle_it 2.888 r_scbond_it 1.879 r_angle_refined_deg 1.616 r_mcangle_it 1.479 r_mcbond_it 0.862 r_nbtor_refined 0.308
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.902 r_dihedral_angle_4_deg 21.106 r_dihedral_angle_3_deg 19.382 r_dihedral_angle_1_deg 6.768 r_scangle_it 2.888 r_scbond_it 1.879 r_angle_refined_deg 1.616 r_mcangle_it 1.479 r_mcbond_it 0.862 r_nbtor_refined 0.308 r_symmetry_vdw_refined 0.249 r_nbd_refined 0.224 r_symmetry_hbond_refined 0.21 r_xyhbond_nbd_refined 0.173 r_chiral_restr 0.109 r_bond_refined_d 0.014 r_gen_planes_refined 0.006 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_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5192 Nucleic Acid Atoms Solvent Atoms 124 Heterogen Atoms 58
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling CNS phasing