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Crystal structure of human RECQL5 helicase APO form in complex with engineered nanobody (Gluebody) G4-043
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 sodium chloride -- 25% PEG3350 -- 0.1M HEPES pH 7.5
Crystal Properties Matthews coefficient Solvent content 3.22 61.76
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 81.909 α = 90 b = 90.121 β = 90 c = 216.571 γ = 90
Symmetry Space Group I 2 2 2
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 2020-10-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.9763 Diamond I03
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 2.17 41.6 99.6 1 7.2 13.3 42737
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 2.17 2.21 0.5
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 2.7 40.988 22465 1151 99.929 0.237 0.235 0.2353 0.2762 0.2673 80.715
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] -0.34 0.293 0.047
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.338 r_dihedral_angle_4_deg 18.954 r_dihedral_angle_3_deg 17.086 r_lrange_it 16.667 r_lrange_other 16.666 r_scangle_it 10.846 r_scangle_other 10.844 r_mcangle_it 10.811 r_mcangle_other 10.811 r_dihedral_angle_1_deg 7.382
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.338 r_dihedral_angle_4_deg 18.954 r_dihedral_angle_3_deg 17.086 r_lrange_it 16.667 r_lrange_other 16.666 r_scangle_it 10.846 r_scangle_other 10.844 r_mcangle_it 10.811 r_mcangle_other 10.811 r_dihedral_angle_1_deg 7.382 r_mcbond_it 7.189 r_mcbond_other 7.18 r_scbond_it 7.045 r_scbond_other 7.045 r_angle_refined_deg 1.555 r_angle_other_deg 1.284 r_symmetry_nbd_refined 0.22 r_nbd_refined 0.213 r_nbd_other 0.208 r_xyhbond_nbd_refined 0.206 r_symmetry_nbd_other 0.202 r_symmetry_xyhbond_nbd_refined 0.18 r_nbtor_refined 0.167 r_symmetry_xyhbond_nbd_other 0.127 r_symmetry_nbtor_other 0.082 r_chiral_restr 0.067 r_bond_refined_d 0.006 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4335 Nucleic Acid Atoms Solvent Atoms 38 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement xia2 data reduction Aimless data scaling PHASER phasing