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Structural basis for allosteric substrate specificity regulation in class III ribonucleotide reductases: NRDD in complex with dATP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1B8B 1B8B.PDB
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7.5 30% PEG 400, 0.2M MGCL2, 0.1M HEPES PH 7.5, 5MM DTT
Crystal Properties Matthews coefficient Solvent content 4.34 71.65
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 98.36 α = 90 b = 98.36 β = 90 c = 244.12 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 CCD ADSC CCD BENT MIRROR 1998-07-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X12B NSLS X12B
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 2.75 40 92 0.09 8.7 2.6 29688 61.1
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 2.75 2.81 70 0.358 1
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 1B8B.PDB 2.75 29.87 29676 2512 92.6 0.215 0.215 0.212 0.258 0.2539 RANDOM 50.2
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] 3.44 3.44 -6.89
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 23.2 c_scangle_it 4.31 c_mcangle_it 2.88 c_scbond_it 2.88 c_angle_deg 1.8 c_mcbond_it 1.78 c_improper_angle_d 0.98 c_bond_d 0.013 c_bond_d_na c_bond_d_prot
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 23.2 c_scangle_it 4.31 c_mcangle_it 2.88 c_scbond_it 2.88 c_angle_deg 1.8 c_mcbond_it 1.78 c_improper_angle_d 0.98 c_bond_d 0.013 c_bond_d_na c_bond_d_prot c_angle_d c_angle_d_na c_angle_d_prot c_angle_deg_na c_angle_deg_prot c_dihedral_angle_d_na c_dihedral_angle_d_prot c_improper_angle_d_na c_improper_angle_d_prot
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4427 Nucleic Acid Atoms Solvent Atoms 58 Heterogen Atoms 32
Software Software Software Name Purpose CNS refinement DENZO data reduction SCALEPACK data scaling CNS phasing