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Plasmodium falciparum apicoplast DNA polymerase (exo-minus) without affinity tag
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5DKU
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 277 Equal parts protein and precipitant solutions.
Protein solution: 20 mg/ml protein, 20 mM Tris, pH 8.0, 500 mM NaCl, 10% glycerol and 5 mM imidazole.
Precipitant solution: PEG 1000 30% (v/v), 100 sodium citrate tribasic dihydrate, pH 5.5, 400 mM NaCl.
Crystal Properties Matthews coefficient Solvent content 3.4 63.82
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 145.369 α = 90 b = 145.369 β = 90 c = 164.944 γ = 120
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 PILATUS3 6M 2018-11-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 23-ID-D 1.0 APS 23-ID-D
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) CC (Half) 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 2.7 19.91 100 0.99 0.8 6.7 54200 61.4
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.7 2.75 0.539
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 5DKU 2.7 19.91 1.35 54063 2005 99.89 0.1918 0.1905 0.1899 0.2237 0.2237 72.97
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 10.28 f_angle_d 0.552 f_chiral_restr 0.042 f_bond_d 0.0043 f_plane_restr 0.0036
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9538 Nucleic Acid Atoms Solvent Atoms 371 Heterogen Atoms 72
Software Software Software Name Purpose PHENIX refinement HKL-3000 data reduction HKL-3000 data scaling PHENIX phasing