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E. coli PriA helicase winged helix domain deletion protein
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4NL4 4NL4 removing the winged helix domain
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 297 50 mM HEPES-HCl pH 7.5, 9.5 % PEG 4000, 4 % Isopropanol, 8 % glycerol, 50 mM sodium malonate, and 25-100 mM sodium fluoride
Crystal Properties Matthews coefficient Solvent content 2.32 46.93
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 69.132 α = 90 b = 56.505 β = 97.67 c = 195.863 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 EIGER X 9M 2016-11-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-D 1.12712 APS 21-ID-D
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim 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 1.978 48.832 96.75 0.05904 0.06941 0.03598 0.998 11.18 3.7 101849 47.4
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.978 2.049 94.98 1.299 1.513 0.7657 0.374 1.03 3.7
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 4NL4 removing the winged helix domain 1.978 48.832 1.34 101832 5084 96.76 0.1871 0.1856 0.19 0.215 0.219
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 14.922 f_angle_d 1.177 f_chiral_restr 0.059 f_bond_d 0.012 f_plane_restr 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9390 Nucleic Acid Atoms Solvent Atoms 412 Heterogen Atoms 44
Software Software Software Name Purpose PHENIX refinement XDS data reduction XDS data scaling PHASER phasing