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Structures of Yeast Ribonucleotide Reductase I
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 = 109.511 α = 90 b = 117.166 β = 90 c = 63.362 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 2004-06-02 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RUH3R 1.5418, 0.91900, 0.91940
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 2.6 50 97.6 0.072 0.072 20.1 3.3 23818 23818
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) 2.6 2.69 98.9 0.445 0.445 2.4 3.1 3098
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 MAD THROUGHOUT 2.6 50 22679 2547 97.76 0.21071 0.20436 0.2035 0.26693 0.2661 RANDOM 51.692
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] -0.12 -3.09 3.21
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.521 r_dihedral_angle_3_deg 19.012 r_dihedral_angle_4_deg 15.267 r_dihedral_angle_1_deg 6.148 r_scangle_it 2.546 r_scbond_it 1.598 r_angle_refined_deg 1.47 r_mcangle_it 1.419 r_mcbond_it 0.791 r_nbtor_refined 0.318
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.521 r_dihedral_angle_3_deg 19.012 r_dihedral_angle_4_deg 15.267 r_dihedral_angle_1_deg 6.148 r_scangle_it 2.546 r_scbond_it 1.598 r_angle_refined_deg 1.47 r_mcangle_it 1.419 r_mcbond_it 0.791 r_nbtor_refined 0.318 r_symmetry_vdw_refined 0.272 r_nbd_refined 0.236 r_xyhbond_nbd_refined 0.182 r_chiral_restr 0.105 r_symmetry_hbond_refined 0.105 r_bond_refined_d 0.013 r_gen_planes_refined 0.005 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 5254 Nucleic Acid Atoms Solvent Atoms 181 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling SOLVE phasing