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Structural mechanism of allosteric substrate specificity in a ribonucleotide reductase: dTTP complex
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1XJE pdb ENTRY 1XJE
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 2.58 55
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 118.438 α = 90 b = 123.776 β = 103.64 c = 106.241 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 2003-08-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE X13 0.804 EMBL/DESY, HAMBURG X13
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 2.4 20 99.6 0.115 8.4 3.8 58198 57953
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) 2.4 2.6 99.5 0.337 3.9 3.8
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 1XJE 2.4 19.98 54841 2969 99.58 0.18767 0.18444 0.183 0.24654 0.244 RANDOM 35.402
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] 2.5 1.32 0.35 -2.23
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.176 r_dihedral_angle_4_deg 18.733 r_dihedral_angle_3_deg 18.609 r_dihedral_angle_1_deg 6.779 r_scangle_it 3.631 r_scbond_it 2.337 r_angle_refined_deg 1.718 r_mcangle_it 1.535 r_mcbond_it 0.875 r_symmetry_hbond_refined 0.484
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.176 r_dihedral_angle_4_deg 18.733 r_dihedral_angle_3_deg 18.609 r_dihedral_angle_1_deg 6.779 r_scangle_it 3.631 r_scbond_it 2.337 r_angle_refined_deg 1.718 r_mcangle_it 1.535 r_mcbond_it 0.875 r_symmetry_hbond_refined 0.484 r_nbtor_refined 0.307 r_metal_ion_refined 0.276 r_nbd_refined 0.215 r_symmetry_vdw_refined 0.2 r_xyhbond_nbd_refined 0.166 r_chiral_restr 0.115 r_bond_refined_d 0.017 r_gen_planes_refined 0.006 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 9828 Nucleic Acid Atoms Solvent Atoms 300 Heterogen Atoms 118
Software Software Software Name Purpose REFMAC refinement MAR345 data collection XDS data scaling