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Crystal structure of helicase Pif1 from Thermus oshimai in complex with oligo GGTTTGGTTTGGTT
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6S3M
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 8.5 298 Tris-HCl 0.1M
NaF 0.03M
NaI 0.03M
NaBr 0.03M
MES 0.03M
PEG 4K 10%
Crystal Properties Matthews coefficient Solvent content 2.42 49.12
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 88.052 α = 90 b = 103.438 β = 90 c = 251.566 γ = 90
Symmetry Space Group C 2 2 21
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 ADSC QUANTUM 315r 2016-05-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL17U1 0.979150 SSRF BL17U1
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 2.21 125.783 99.58 0.077 0.083 0.031 0.999 13.6 6.9 404851 50.9
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 2.21 2.25 51 1.126 1.217 0.457 0.812 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 6S3M 2.21 44.02 1.37 55166 2768 95.97 0.1812 0.1791 0.1818 0.2203 0.2225 70.02
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 22.7105 f_angle_d 1.387 f_chiral_restr 0.072 f_bond_d 0.0108 f_plane_restr 0.0084
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7008 Nucleic Acid Atoms 289 Solvent Atoms 110 Heterogen Atoms 67
Software Software Software Name Purpose PHENIX refinement PHENIX refinement XDS data reduction Aimless data scaling PHASER phasing