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Crystal structure of human Pif1 helicase, apoform.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6HPH
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 277 Li2SO4, PEG 2K MME, MES
Crystal Properties Matthews coefficient Solvent content 2.48 50.34
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 63.54 α = 90 b = 81.4 β = 90 c = 91.48 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 SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.92819 Diamond I04
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 1.44 81.4 99.9 0.045 0.999 15.9 6.6 86350 34.9
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 1.44 1.48 99.9 1.329 0.514 6.8
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 6HPH 1.44 60.89 81905 4365 99.83 0.13692 0.13372 0.19468 0.2134 RANDOM 34.849
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] -0.58 1.3 -0.72
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 43.167 r_dihedral_angle_2_deg 38.729 r_sphericity_bonded 21.119 r_dihedral_angle_4_deg 19.174 r_dihedral_angle_3_deg 16.086 r_long_range_B_refined 9.142 r_scangle_other 8.614 r_scbond_other 8.118 r_scbond_it 8.097 r_long_range_B_other 7.848
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 43.167 r_dihedral_angle_2_deg 38.729 r_sphericity_bonded 21.119 r_dihedral_angle_4_deg 19.174 r_dihedral_angle_3_deg 16.086 r_long_range_B_refined 9.142 r_scangle_other 8.614 r_scbond_other 8.118 r_scbond_it 8.097 r_long_range_B_other 7.848 r_dihedral_angle_1_deg 6.614 r_mcangle_it 5.886 r_mcangle_other 5.886 r_rigid_bond_restr 5.55 r_mcbond_it 5.217 r_mcbond_other 5.214 r_angle_refined_deg 2.452 r_angle_other_deg 1.288 r_chiral_restr 0.175 r_bond_refined_d 0.029 r_gen_planes_refined 0.013 r_bond_other_d 0.003 r_gen_planes_other 0.003 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 3172 Nucleic Acid Atoms Solvent Atoms 976 Heterogen Atoms 15
Software Software Software Name Purpose REFMAC refinement xia2 data reduction xia2 data scaling MOLREP phasing