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Structural mechanism of allosteric substrate specificity in a ribonucleotide reductase: dTTP-GDP complex
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1R1R pdb entry 1R1R
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.5 293 PEG8000, sodium acetate, sodium chloride, dithiotreithol, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.63 53.32
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 119.391 α = 90 b = 124.376 β = 103.68 c = 107.243 γ = 90
Symmetry Space Group C 1 2 1
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 MARRESEARCH 2002-08-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE X11 0.811 EMBL/DESY, HAMBURG X11
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.9 18 97.2 0.07 12.23 2.7 119507
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.9 1.97 96.6 0.399 3.2
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 pdb entry 1R1R 1.9 18 110169 5794 97.16 0.18445 0.18241 0.1906 0.22268 0.2314 RANDOM 31.972
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] 1.96 1.3 0.4 -1.74
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.73 r_dihedral_angle_4_deg 19.657 r_dihedral_angle_3_deg 16.342 r_dihedral_angle_1_deg 6.898 r_scangle_it 3.66 r_scbond_it 2.633 r_angle_refined_deg 1.78 r_mcangle_it 1.595 r_mcbond_it 1.375 r_angle_other_deg 0.948
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.73 r_dihedral_angle_4_deg 19.657 r_dihedral_angle_3_deg 16.342 r_dihedral_angle_1_deg 6.898 r_scangle_it 3.66 r_scbond_it 2.633 r_angle_refined_deg 1.78 r_mcangle_it 1.595 r_mcbond_it 1.375 r_angle_other_deg 0.948 r_symmetry_vdw_other 0.337 r_symmetry_vdw_refined 0.275 r_mcbond_other 0.267 r_nbd_refined 0.221 r_nbd_other 0.187 r_symmetry_hbond_refined 0.185 r_nbtor_refined 0.183 r_xyhbond_nbd_refined 0.165 r_metal_ion_refined 0.133 r_chiral_restr 0.125 r_nbtor_other 0.089 r_bond_refined_d 0.019 r_xyhbond_nbd_other 0.018 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 10001 Nucleic Acid Atoms Solvent Atoms 791 Heterogen Atoms 122
Software Software Software Name Purpose REFMAC refinement MAR345 data collection SCALEPACK data scaling