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The crystal structure of the L439V variant of Pol2CORE in complex with DNA and an incoming nucleotide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4M8O
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 292 8 % PEG 20K , 150 mM NaAc, 0-1,5% Glycerol, 50 mM MES pH6.5
Crystal Properties Matthews coefficient Solvent content 2.87 57.14
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 221.505 α = 90 b = 70.685 β = 100.14 c = 111.639 γ = 90
Symmetry Space Group C 1 2 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 EIGER X 4M 2020-03-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON MAX IV BEAMLINE BioMAX 0.976254 MAX IV BioMAX
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Rrim I (All) 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 2.46 45.78 99.8 0.944 0.997 7.95 4.25 61906 56.4
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.46 2.65 99.9 0.944 0.596 0.97 4.25
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 4m8o 2.46 45.78 58947 3070 99.83 0.2119 0.2095 0.2126 0.2562 0.2546 RANDOM 73.254
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] -2.31 0.23 1.13 1.03
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.502 r_dihedral_angle_4_deg 21.528 r_dihedral_angle_3_deg 18.397 r_dihedral_angle_1_deg 6.993 r_angle_refined_deg 1.672 r_angle_other_deg 1.297 r_chiral_restr 0.085 r_bond_refined_d 0.011 r_gen_planes_refined 0.008 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.502 r_dihedral_angle_4_deg 21.528 r_dihedral_angle_3_deg 18.397 r_dihedral_angle_1_deg 6.993 r_angle_refined_deg 1.672 r_angle_other_deg 1.297 r_chiral_restr 0.085 r_bond_refined_d 0.011 r_gen_planes_refined 0.008 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9036 Nucleic Acid Atoms 529 Solvent Atoms 96 Heterogen Atoms 36
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling PDB_EXTRACT data extraction PHASER phasing