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Crystal structure of human Pif1 helicase in complex with AMP-PNP, brominated crystal form.
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 277 Na-acetate, PEG 2K MME, Tris-Cl
Crystal Properties Matthews coefficient Solvent content 2.2 44.2
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 73.25 α = 90 b = 76.82 β = 90 c = 142.54 γ = 90
Symmetry Space Group P 21 21 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 PIXEL DECTRIS PILATUS3 S 6M 2015-10-02 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.91966, 0.91992, 0.91912 Diamond I03
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 1.43 73.25 99.9 0.146 0.999 9.6 12.8 148682 20.2
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.43 1.47 99.8 2.316 0.598 10.7
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 THROUGHOUT 1.43 71.37 141225 7357 99.89 0.22579 0.22366 0.2219 0.26633 0.265 RANDOM 18.412
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] -0.37 0.37
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 39.992 r_dihedral_angle_2_deg 31.815 r_dihedral_angle_4_deg 22.61 r_sphericity_bonded 18.391 r_dihedral_angle_3_deg 15.092 r_long_range_B_refined 6.347 r_dihedral_angle_1_deg 6.23 r_long_range_B_other 5.081 r_scangle_other 4.865 r_scbond_it 4.186
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 39.992 r_dihedral_angle_2_deg 31.815 r_dihedral_angle_4_deg 22.61 r_sphericity_bonded 18.391 r_dihedral_angle_3_deg 15.092 r_long_range_B_refined 6.347 r_dihedral_angle_1_deg 6.23 r_long_range_B_other 5.081 r_scangle_other 4.865 r_scbond_it 4.186 r_scbond_other 4.186 r_mcangle_other 3.547 r_mcangle_it 3.54 r_rigid_bond_restr 3.158 r_mcbond_it 2.73 r_mcbond_other 2.711 r_angle_refined_deg 1.958 r_angle_other_deg 1.573 r_chiral_restr 0.104 r_bond_refined_d 0.014 r_gen_planes_refined 0.012 r_gen_planes_other 0.005 r_bond_other_d 0.002 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6338 Nucleic Acid Atoms Solvent Atoms 1197 Heterogen Atoms 73
Software Software Software Name Purpose REFMAC refinement xia2 data reduction xia2 data scaling SHELXDE phasing