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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 = 107.866 α = 90 b = 117.593 β = 90 c = 64.884 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 2005-03-31 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 2.9 50 96.9 0.128 0.128 13.5 5.5 18449 18449
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) 2.9 3 99.8 0.414 0.414 2.6 5.4 2551
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 2.9 50 16485 1871 96.98 0.18409 0.17726 0.1787 0.24462 0.2428 RANDOM 28.205
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] -0.96 -1.98 2.94
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.178 r_dihedral_angle_3_deg 19.697 r_dihedral_angle_4_deg 17.375 r_dihedral_angle_1_deg 6.273 r_scangle_it 2.544 r_scbond_it 1.576 r_angle_refined_deg 1.523 r_mcangle_it 1.281 r_mcbond_it 0.717 r_nbtor_refined 0.317
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.178 r_dihedral_angle_3_deg 19.697 r_dihedral_angle_4_deg 17.375 r_dihedral_angle_1_deg 6.273 r_scangle_it 2.544 r_scbond_it 1.576 r_angle_refined_deg 1.523 r_mcangle_it 1.281 r_mcbond_it 0.717 r_nbtor_refined 0.317 r_nbd_refined 0.233 r_symmetry_vdw_refined 0.204 r_xyhbond_nbd_refined 0.169 r_symmetry_hbond_refined 0.119 r_chiral_restr 0.104 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 5208 Nucleic Acid Atoms Solvent Atoms 138 Heterogen Atoms 57
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling CNS phasing