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Dna polymerase beta with a gapped DND substrate and dTMP(CF2)PP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2FMS PDB entry 2FMS
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8 291 100 mM IMIDAZOLE,pH 8.0, SODIUM ACETATE 350 mM, PEG2000 MONOMETHYL ETHER 20%, VAPOR DIFFUSION, SITTING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 2.2 44.2
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 50.5 α = 90 b = 79.7 β = 107.9 c = 55.3 γ = 90
Symmetry Space Group P 1 21 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 RIGAKU SATURN 92 VIRAMAX 2005-04-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 HF 1.5418
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 2.2 50 86.4 0.098 9.2 2.3 18597 18597 -3 17.5
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) 2.2 2.28 82.2 0.438 2.28 2.5 1757
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 2FMS 2.2 20.58 15889 1559 74.9 0.208 0.208 0.1891 0.266 0.2536 RANDOM 29.8
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] 2.09 5.36 -1.14 -0.94
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 24 c_scangle_it 2.89 c_mcangle_it 2.14 c_scbond_it 1.92 c_mcbond_it 1.34 c_angle_deg 1.1 c_improper_angle_d 1.01 c_bond_d 0.006 c_bond_d_na c_bond_d_prot
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 24 c_scangle_it 2.89 c_mcangle_it 2.14 c_scbond_it 1.92 c_mcbond_it 1.34 c_angle_deg 1.1 c_improper_angle_d 1.01 c_bond_d 0.006 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 2656 Nucleic Acid Atoms 631 Solvent Atoms 277 Heterogen Atoms 37
Software Software Software Name Purpose HKL-2000 data collection CNS refinement HKL-2000 data reduction HKL-2000 data scaling CNS phasing