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Crystal structure of human RECQL5 helicase APO form in complex with engineered nanobody (Gluebody) G5-006
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5LB5
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 293 0.2M ammonium sulfate -- 25% PEG3350 -- 0.1M HEPES pH 7.5
Crystal Properties Matthews coefficient Solvent content 3.23 61.89
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 232.589 α = 90 b = 89.965 β = 110.058 c = 164.126 γ = 90
Symmetry Space Group C 1 2 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 PILATUS3 6M 2021-02-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 0.9119 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 2 109.23 97.7 1 13.9 2.9 209231
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 2 2.04 87.3 0.3
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 5LB5 2.002 77.687 208891 10399 97.572 0.245 0.2431 0.2474 0.2747 0.2776 48.403
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] 0.018 0.005 -0.02 -0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.17 r_dihedral_angle_4_deg 17.464 r_dihedral_angle_3_deg 16.197 r_lrange_other 10.892 r_lrange_it 10.888 r_scangle_it 7.681 r_scangle_other 7.672 r_dihedral_angle_1_deg 6.856 r_mcangle_it 5.958 r_mcangle_other 5.958
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.17 r_dihedral_angle_4_deg 17.464 r_dihedral_angle_3_deg 16.197 r_lrange_other 10.892 r_lrange_it 10.888 r_scangle_it 7.681 r_scangle_other 7.672 r_dihedral_angle_1_deg 6.856 r_mcangle_it 5.958 r_mcangle_other 5.958 r_scbond_it 5.121 r_scbond_other 5.084 r_mcbond_it 4.158 r_mcbond_other 4.158 r_angle_refined_deg 1.443 r_angle_other_deg 1.334 r_symmetry_nbd_refined 0.254 r_nbd_other 0.219 r_nbd_refined 0.202 r_symmetry_nbd_other 0.18 r_nbtor_refined 0.162 r_xyhbond_nbd_refined 0.161 r_symmetry_xyhbond_nbd_refined 0.145 r_symmetry_nbtor_other 0.078 r_ncsr_local_group_9 0.078 r_ncsr_local_group_11 0.07 r_ncsr_local_group_8 0.069 r_chiral_restr 0.065 r_ncsr_local_group_5 0.062 r_ncsr_local_group_10 0.061 r_ncsr_local_group_12 0.061 r_ncsr_local_group_3 0.059 r_ncsr_local_group_1 0.058 r_ncsr_local_group_7 0.058 r_ncsr_local_group_2 0.056 r_ncsr_local_group_6 0.056 r_ncsr_local_group_4 0.054 r_symmetry_xyhbond_nbd_other 0.035 r_bond_refined_d 0.007 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 17422 Nucleic Acid Atoms Solvent Atoms 1028 Heterogen Atoms 20
Software Software Software Name Purpose REFMAC refinement xia2 data reduction Aimless data scaling PHASER phasing