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Crystal structure of human RECQL5 helicase APO form in complex with engineered nanobody (Gluebody) G2-001
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 6.5 293 0.2M sodium chloride -- 25% PEG3350 -- 0.1M bis-tris pH 6.5
Crystal Properties Matthews coefficient Solvent content 2.68 54.13
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 76.612 α = 90 b = 183.969 β = 108.124 c = 100.947 γ = 90
Symmetry Space Group P 1 21 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 2019-10-21 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 2.5 183.84 99.2 1 8.6 2.7 95510
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 2.5 2.55 0.61
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 2.5 95.938 90975 4407 99.371 0.238 0.2356 0.2386 0.2806 0.2824 79.866
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] 0.817 -2.886 1.73 -0.541
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.553 r_lrange_other 18.155 r_lrange_it 18.154 r_dihedral_angle_3_deg 16.321 r_dihedral_angle_4_deg 16.143 r_mcangle_it 11.838 r_mcangle_other 11.837 r_scangle_it 11.791 r_scangle_other 11.791 r_mcbond_it 8.053
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.553 r_lrange_other 18.155 r_lrange_it 18.154 r_dihedral_angle_3_deg 16.321 r_dihedral_angle_4_deg 16.143 r_mcangle_it 11.838 r_mcangle_other 11.837 r_scangle_it 11.791 r_scangle_other 11.791 r_mcbond_it 8.053 r_mcbond_other 8.047 r_scbond_it 7.763 r_scbond_other 7.763 r_dihedral_angle_1_deg 6.464 r_angle_refined_deg 1.411 r_angle_other_deg 1.248 r_symmetry_nbd_refined 0.401 r_nbd_other 0.327 r_symmetry_xyhbond_nbd_refined 0.304 r_nbd_refined 0.202 r_symmetry_nbd_other 0.178 r_xyhbond_nbd_refined 0.166 r_nbtor_refined 0.158 r_symmetry_xyhbond_nbd_other 0.143 r_xyhbond_nbd_other 0.124 r_ncsr_local_group_7 0.098 r_ncsr_local_group_11 0.097 r_ncsr_local_group_8 0.094 r_ncsr_local_group_12 0.094 r_ncsr_local_group_6 0.09 r_ncsr_local_group_4 0.088 r_ncsr_local_group_3 0.087 r_ncsr_local_group_2 0.085 r_ncsr_local_group_9 0.085 r_ncsr_local_group_10 0.083 r_ncsr_local_group_1 0.081 r_ncsr_local_group_5 0.081 r_symmetry_nbtor_other 0.076 r_chiral_restr 0.06 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 17546 Nucleic Acid Atoms Solvent Atoms 95 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement xia2 data reduction Aimless data scaling PHASER phasing