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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 = 107.759 α = 90 b = 117.509 β = 90 c = 64.584 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 2005-03-29 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 99.7 0.127 0.127 13.6 4.6 18752 18752
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 3 100 0.408 0.408 2.1 4.7 2553
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 16829 1901 99.58 0.18331 0.17728 0.1778 0.23595 0.2355 RANDOM 37.403
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] -1.5 -2.13 3.63
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.786 r_dihedral_angle_3_deg 20.339 r_dihedral_angle_4_deg 19.698 r_dihedral_angle_1_deg 6.862 r_scangle_it 2.466 r_angle_refined_deg 1.591 r_scbond_it 1.501 r_mcangle_it 1.25 r_mcbond_it 0.705 r_nbtor_refined 0.319
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.786 r_dihedral_angle_3_deg 20.339 r_dihedral_angle_4_deg 19.698 r_dihedral_angle_1_deg 6.862 r_scangle_it 2.466 r_angle_refined_deg 1.591 r_scbond_it 1.501 r_mcangle_it 1.25 r_mcbond_it 0.705 r_nbtor_refined 0.319 r_nbd_refined 0.236 r_symmetry_vdw_refined 0.211 r_xyhbond_nbd_refined 0.165 r_chiral_restr 0.109 r_symmetry_hbond_refined 0.073 r_metal_ion_refined 0.044 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_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 133 Heterogen Atoms 57
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling CNS phasing