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Fidelity of Dpo4: effect of metal ions, nucleotide selection and pyrophosphorolysis
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1JX4 PDB ENTRY 1JX4
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7 pH 7.0
Crystal Properties Matthews coefficient Solvent content 2.75 55.25
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 98.101 α = 90 b = 103.009 β = 90 c = 52.399 γ = 90
Symmetry Space Group P 21 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 95 IMAGE PLATE RIGAKU RAXIS IV MIRROR 2004-12-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RU200
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 2.1 30 95.1 0.06 13.9 2.44 30510 29.5
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) 2.1 2.14 87.6 0.406 1.49 2.3
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) 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 1JX4 2.1 26.79 33308 30510 1438 91.6 0.227 0.227 0.227 0.254 0.2552 RANDOM 45.1
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] 9.93 -4.44 -5.49
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 20.9 c_scangle_it 3.2 c_mcangle_it 2.23 c_scbond_it 2.09 c_mcbond_it 1.37 c_angle_deg 1.2 c_improper_angle_d 0.94 c_bond_d 0.007 c_bond_d_na c_bond_d_prot
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 20.9 c_scangle_it 3.2 c_mcangle_it 2.23 c_scbond_it 2.09 c_mcbond_it 1.37 c_angle_deg 1.2 c_improper_angle_d 0.94 c_bond_d 0.007 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 2744 Nucleic Acid Atoms 606 Solvent Atoms 160 Heterogen Atoms 33
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling CNS refinement PDB_EXTRACT data extraction CNS phasing