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XChem refined PIF1-x0076 complex
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 277.15 XChem 0.045uls compound (0.5M) in DMSO echo dispensed into crystal drop
Drop = 0.3uls protein + 0.3us well +0.001uls seeds.
Protein = 25uls 30mgs/ml human PIF1 (206-620) in 10mM Tris pH 7.5, 175mM NaCl, 2%glycerol, 5mM DTT, 0.1mM PMSF + 21uls 10mM Tris, 2.7uls 0.2M MgCl2, 5uls 100mM AMPPNP + 27uls H2O.
Well = 4% Glycerol, 27% PEG 2KMME, 0.1M NaAcetate, 0.1M Tris pH8.5.
Set up on douglas instruments robot - tray on ice - set-up room temperature - crystallised 4 degrees C.
Crystal Properties Matthews coefficient Solvent content 2.24 45.11
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 73.6 α = 90 b = 143.714 β = 90 c = 77.238 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 PIXEL DECTRIS PILATUS 6M-F 2018-03-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 0.91587 Diamond I04-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.727 27.83 99.6 0.999 19.5 6.5 43220
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.73 1.77 0.866
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 (All) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION FOURIER SYNTHESIS THROUGHOUT 1.727 27.83 43195 2134 99.617 0.175 0.1734 0.2114 0.1923 30.663
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] -2.208 0.903 1.304
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 16.622 r_dihedral_angle_3_deg 13.335 r_dihedral_angle_2_deg 9.591 r_lrange_it 7.677 r_scangle_it 6.015 r_dihedral_angle_1_deg 5.641 r_scbond_it 4.131 r_mcangle_it 3.331 r_mcbond_it 2.479 r_angle_refined_deg 1.896
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 16.622 r_dihedral_angle_3_deg 13.335 r_dihedral_angle_2_deg 9.591 r_lrange_it 7.677 r_scangle_it 6.015 r_dihedral_angle_1_deg 5.641 r_scbond_it 4.131 r_mcangle_it 3.331 r_mcbond_it 2.479 r_angle_refined_deg 1.896 r_nbtor_refined 0.309 r_nbd_refined 0.23 r_xyhbond_nbd_refined 0.189 r_symmetry_nbd_refined 0.165 r_symmetry_xyhbond_nbd_refined 0.14 r_chiral_restr 0.122 r_bond_refined_d 0.009 r_gen_planes_refined 0.009
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3150 Nucleic Acid Atoms Solvent Atoms 373 Heterogen Atoms 68
Software Software Software Name Purpose REFMAC refinement DIALS data reduction DIALS data scaling REFMAC phasing