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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 293 0.2M sodium formate -- 20% PEG3350
Crystal Properties Matthews coefficient Solvent content 3.25 62.1
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 82.355 α = 90 b = 90.675 β = 90.754 c = 217.853 γ = 90
Symmetry Space Group I 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 2020-04-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.9762 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 2.13 60.94 99.3 0.9 9 6.9 89383
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 2.13 2.16 95 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 2.3 56.743 71015 3471 99.533 0.265 0.2636 0.2571 0.291 0.2685 72.529
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] 5.36 6.029 -6.964 1.444
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.04 r_lrange_it 18.008 r_lrange_other 18.008 r_dihedral_angle_3_deg 16.663 r_dihedral_angle_4_deg 14.423 r_mcangle_other 12.481 r_mcangle_it 12.479 r_scangle_it 12.11 r_scangle_other 12.11 r_mcbond_it 8.513
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.04 r_lrange_it 18.008 r_lrange_other 18.008 r_dihedral_angle_3_deg 16.663 r_dihedral_angle_4_deg 14.423 r_mcangle_other 12.481 r_mcangle_it 12.479 r_scangle_it 12.11 r_scangle_other 12.11 r_mcbond_it 8.513 r_mcbond_other 8.499 r_scbond_it 7.889 r_scbond_other 7.888 r_dihedral_angle_1_deg 6.764 r_angle_refined_deg 1.522 r_angle_other_deg 1.304 r_nbd_other 0.245 r_symmetry_xyhbond_nbd_refined 0.211 r_nbd_refined 0.199 r_symmetry_nbd_other 0.184 r_ncsr_local_group_2 0.178 r_symmetry_nbd_refined 0.174 r_nbtor_refined 0.161 r_xyhbond_nbd_refined 0.143 r_symmetry_nbtor_other 0.08 r_ncsr_local_group_1 0.076 r_chiral_restr 0.069 r_symmetry_xyhbond_nbd_other 0.059 r_bond_refined_d 0.007 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 8729 Nucleic Acid Atoms Solvent Atoms 83 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement xia2 data reduction Aimless data scaling PHASER phasing