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STRUCTURAL BASIS FOR ALLOSTERIC SUBSTRATE SPECIFICITY REGULATION IN CLASS III RIBONUCLEOTIDE REDUCTASES: NRDD IN COMPLEX WITH DGTP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1B8B PDB ENTRY 1B8B
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7.5 30% PEG 400, 02M MGCL2, 0.1M HEPES PH 7.5, 7MM DTT
Crystal Properties Matthews coefficient Solvent content 4.5 72.4
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 98.163 α = 90 b = 98.163 β = 90 c = 246.131 γ = 90
Symmetry Space Group P 43 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 MARRESEARCH BENT MIRROR 1999-05-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON MAX II BEAMLINE I711 MAX II I711
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 2.43 37.8 95.6 0.096 15.3 3.7 44361
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.43 2.49 94.1 0.274 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-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 1B8B 2.45 20.08 39943 1742 95.7 0.204 0.2108 0.246 0.2272 RANDOM 41.49
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] -0.04 -0.04 0.09
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 6.203 r_mcangle_it 3.173 r_scangle_it 3.136 r_scbond_it 2.048 r_mcbond_it 1.983 r_angle_refined_deg 1.397 r_angle_other_deg 0.818 r_symmetry_vdw_other 0.268 r_symmetry_vdw_refined 0.258 r_nbd_other 0.219
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 6.203 r_mcangle_it 3.173 r_scangle_it 3.136 r_scbond_it 2.048 r_mcbond_it 1.983 r_angle_refined_deg 1.397 r_angle_other_deg 0.818 r_symmetry_vdw_other 0.268 r_symmetry_vdw_refined 0.258 r_nbd_other 0.219 r_symmetry_hbond_refined 0.216 r_xyhbond_nbd_refined 0.196 r_nbd_refined 0.186 r_nbtor_other 0.085 r_chiral_restr 0.077 r_metal_ion_refined 0.015 r_bond_refined_d 0.011 r_gen_planes_refined 0.005 r_gen_planes_other 0.003 r_bond_other_d 0.002 r_dihedral_angle_2_deg r_dihedral_angle_3_deg r_dihedral_angle_4_deg r_nbtor_refined r_xyhbond_nbd_other r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4411 Nucleic Acid Atoms Solvent Atoms 228 Heterogen Atoms 64
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling CNS phasing