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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 = 108.321 α = 90 b = 117.682 β = 90 c = 64.518 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 2005-03-22 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 2.6 50 99.8 0.11 0.11 7.3 7 26145 26145
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 2.69 100 0.736 0.736 2.6 7.1 2587
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 2.6 50 23454 2626 99.6 0.20738 0.20147 0.1993 0.26011 0.2576 RANDOM 46.4
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_angle_refined_deg 1.728 r_bond_refined_d 0.016 r_dihedral_angle_1_deg r_dihedral_angle_2_deg r_dihedral_angle_3_deg r_dihedral_angle_4_deg r_chiral_restr r_gen_planes_refined r_nbd_refined r_nbtor_refined
RMS Deviations Key Refinement Restraint Deviation r_angle_refined_deg 1.728 r_bond_refined_d 0.016 r_dihedral_angle_1_deg r_dihedral_angle_2_deg r_dihedral_angle_3_deg r_dihedral_angle_4_deg r_chiral_restr r_gen_planes_refined r_nbd_refined r_nbtor_refined r_xyhbond_nbd_refined r_symmetry_vdw_refined r_symmetry_hbond_refined r_mcbond_it r_mcangle_it r_scbond_it r_scangle_it
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5183 Nucleic Acid Atoms Solvent Atoms 58 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling CNS phasing