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Crystal structure of human RECQL5 helicase APO form in complex with engineered nanobody (Gluebody) G2*-011
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 lithium sulfate -- 25% PEG3350 -- 0.1M HEPES pH 7.5
Crystal Properties Matthews coefficient Solvent content 3.96 68.91
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 114.89 α = 90 b = 198.954 β = 90 c = 172.926 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 PILATUS3 6M 2020-01-17 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 3.04 99.54 100 0.9 3.4 6.6 38564
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 3.04 3.09 0.2
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 3.3 99.493 30125 1461 99.861 0.245 0.2431 0.2428 0.292 0.2901 75.806
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] 0.017 0.069 -0.086
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 27.725 r_dihedral_angle_3_deg 18.878 r_dihedral_angle_4_deg 17.298 r_lrange_other 14.463 r_lrange_it 14.462 r_mcangle_it 8.001 r_mcangle_other 8 r_scangle_it 7.834 r_scangle_other 7.806 r_dihedral_angle_1_deg 7.496
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 27.725 r_dihedral_angle_3_deg 18.878 r_dihedral_angle_4_deg 17.298 r_lrange_other 14.463 r_lrange_it 14.462 r_mcangle_it 8.001 r_mcangle_other 8 r_scangle_it 7.834 r_scangle_other 7.806 r_dihedral_angle_1_deg 7.496 r_mcbond_it 4.89 r_mcbond_other 4.89 r_scbond_it 4.657 r_scbond_other 4.638 r_angle_refined_deg 1.589 r_angle_other_deg 1.313 r_symmetry_xyhbond_nbd_refined 0.322 r_symmetry_nbd_refined 0.283 r_nbd_other 0.267 r_nbd_refined 0.218 r_symmetry_nbd_other 0.211 r_nbtor_refined 0.167 r_xyhbond_nbd_refined 0.131 r_ncsr_local_group_1 0.106 r_ncsr_local_group_2 0.1 r_symmetry_nbtor_other 0.085 r_chiral_restr 0.065 r_symmetry_xyhbond_nbd_other 0.034 r_xyhbond_nbd_other 0.033 r_bond_refined_d 0.006 r_gen_planes_refined 0.006 r_bond_other_d 0.003 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8695 Nucleic Acid Atoms Solvent Atoms 59 Heterogen Atoms 25
Software Software Software Name Purpose REFMAC refinement xia2 data reduction Aimless data scaling PHASER phasing