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Structures of Yeast Ribonucloetide 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 4.6 298 sodium acetate, sodium formate, pH 4.6, EVAPORATION, temperature 298K
Crystal Properties Matthews coefficient Solvent content 4.26 72.94
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 433.696 α = 90 b = 433.696 β = 90 c = 433.696 γ = 90
Symmetry Space Group F 41 3 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 CCD ADSC QUANTUM 4 2004-03-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 17-ID 1.0000 APS 17-ID
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 95 0.088 0.088 30.2 11.1 73347 73347
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) 1 2.9 3 93.8 0.476 0.476 2.7 8.7 7455
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 72141 3825 98.42 0.21934 0.21734 0.215 0.25725 0.2535 RANDOM 51.279
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_dihedral_angle_2_deg 36.656 r_dihedral_angle_3_deg 21.312 r_dihedral_angle_4_deg 19.408 r_dihedral_angle_1_deg 7.403 r_scangle_it 2.864 r_scbond_it 1.665 r_angle_refined_deg 1.585 r_mcangle_it 1.432 r_mcbond_it 0.789 r_nbtor_refined 0.323
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.656 r_dihedral_angle_3_deg 21.312 r_dihedral_angle_4_deg 19.408 r_dihedral_angle_1_deg 7.403 r_scangle_it 2.864 r_scbond_it 1.665 r_angle_refined_deg 1.585 r_mcangle_it 1.432 r_mcbond_it 0.789 r_nbtor_refined 0.323 r_nbd_refined 0.239 r_symmetry_vdw_refined 0.198 r_xyhbond_nbd_refined 0.166 r_symmetry_hbond_refined 0.155 r_chiral_restr 0.121 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 12267 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 8
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling PHASER phasing