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Crystal structure of the ternary complex of the D714A mutant of RB69 DNA polymerase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3NGI
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6 298 12% PEG 8000, 0.1 M MES, 0.2 Ammonium Sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 298K, pH 6
Crystal Properties Matthews coefficient Solvent content 2.88 57.24
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 74.258 α = 90 b = 119.353 β = 91.64 c = 148.031 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 PIXEL DECTRIS PILATUS 6M 2013-01-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X25 1.1 NSLS X25
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 2.55 39.3 99.9 0.063 16.8 4.9 84020
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 2.55 2.559 99.8 0.617 2.5 4.8
Refinement Statistics Diffraction ID Structure Solution Method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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 3NGI 2.55 35.334 1.34 83990 4149 99.85 0.1704 0.1682 0.1711 0.2109 0.2102 RANDOM
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 17.24 f_angle_d 1.192 f_chiral_restr 0.081 f_bond_d 0.011 f_plane_restr 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 13909 Nucleic Acid Atoms 1256 Solvent Atoms 304 Heterogen Atoms 169
Software Software Software Name Purpose CBASS data collection PHASER phasing PHENIX refinement XDS data reduction SCALA data scaling