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Crystal structure of human RECQL5 helicase APO form in complex with engineered nanobody (Gluebody) G2*-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 8.5 293 0.2M lithium sulfate -- 25% PEG3350 -- 0.1M tris pH 8.5
Crystal Properties Matthews coefficient Solvent content 3.94 68.79
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 115.13 α = 90 b = 199.086 β = 90 c = 174.158 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 2.41 99.68 100 0.9 8.2 6.7 77373
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 2.41 2.45 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-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 5LB5 2.7 99.665 55150 2899 99.926 0.227 0.225 0.2583 0.2341 61.392
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] 0.557 2.265 -2.822
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.552 r_dihedral_angle_4_deg 22.232 r_dihedral_angle_3_deg 18.074 r_lrange_it 13.871 r_lrange_other 13.87 r_scangle_it 8.495 r_scangle_other 8.49 r_mcangle_it 8.166 r_mcangle_other 8.165 r_dihedral_angle_1_deg 7.229
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.552 r_dihedral_angle_4_deg 22.232 r_dihedral_angle_3_deg 18.074 r_lrange_it 13.871 r_lrange_other 13.87 r_scangle_it 8.495 r_scangle_other 8.49 r_mcangle_it 8.166 r_mcangle_other 8.165 r_dihedral_angle_1_deg 7.229 r_scbond_it 5.49 r_scbond_other 5.476 r_mcbond_other 5.294 r_mcbond_it 5.293 r_angle_refined_deg 1.534 r_angle_other_deg 1.288 r_symmetry_nbd_refined 0.267 r_nbd_other 0.242 r_nbd_refined 0.208 r_xyhbond_nbd_refined 0.194 r_symmetry_nbd_other 0.182 r_nbtor_refined 0.163 r_symmetry_xyhbond_nbd_refined 0.098 r_ncsr_local_group_1 0.083 r_symmetry_nbtor_other 0.078 r_chiral_restr 0.07 r_ncsr_local_group_2 0.068 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 8750 Nucleic Acid Atoms Solvent Atoms 52 Heterogen Atoms 20
Software Software Software Name Purpose REFMAC refinement xia2 data reduction Aimless data scaling PHASER phasing