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Crystal structure of human RECQL5 helicase APO form in complex with engineered nanobody (Gluebody) G1-001
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 5.9 293 0.1M bis-tris pH 5.9 -- 0.1M lithium sulfate -- 30% PEG3350
Crystal Properties Matthews coefficient Solvent content 2.68 54.13
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 75.74 α = 90 b = 185.53 β = 107.47 c = 101.01 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 2018-07-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.9795 Diamond I04
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Rrim I (All) 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 2.79 96.351 99.8 0.083 1 12.9 6.8 65889
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 2.79 2.84 0.5 1.1
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 2.79 96.351 65750 3147 99.58 0.226 0.2238 0.261 0.2554 103.124
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] -2.819 -2.55 0.1 3.609
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.827 r_lrange_it 23.509 r_lrange_other 23.509 r_dihedral_angle_4_deg 17.924 r_dihedral_angle_3_deg 16.808 r_scangle_it 16.126 r_scangle_other 16.091 r_mcangle_it 15.776 r_mcangle_other 15.776 r_mcbond_it 10.956
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.827 r_lrange_it 23.509 r_lrange_other 23.509 r_dihedral_angle_4_deg 17.924 r_dihedral_angle_3_deg 16.808 r_scangle_it 16.126 r_scangle_other 16.091 r_mcangle_it 15.776 r_mcangle_other 15.776 r_mcbond_it 10.956 r_mcbond_other 10.949 r_scbond_it 10.803 r_scbond_other 10.766 r_dihedral_angle_1_deg 6.843 r_angle_refined_deg 1.432 r_angle_other_deg 1.237 r_nbd_other 0.313 r_symmetry_nbd_refined 0.298 r_symmetry_xyhbond_nbd_refined 0.29 r_nbd_refined 0.204 r_symmetry_nbd_other 0.18 r_nbtor_refined 0.162 r_xyhbond_nbd_refined 0.146 r_ncsr_local_group_12 0.118 r_ncsr_local_group_8 0.11 r_ncsr_local_group_10 0.101 r_ncsr_local_group_9 0.096 r_ncsr_local_group_11 0.087 r_symmetry_nbtor_other 0.078 r_ncsr_local_group_3 0.077 r_ncsr_local_group_2 0.075 r_ncsr_local_group_6 0.074 r_ncsr_local_group_1 0.071 r_ncsr_local_group_5 0.068 r_ncsr_local_group_4 0.064 r_ncsr_local_group_7 0.063 r_chiral_restr 0.059 r_symmetry_xyhbond_nbd_other 0.046 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 17587 Nucleic Acid Atoms Solvent Atoms 19 Heterogen Atoms 20
Software Software Software Name Purpose REFMAC refinement xia2 data reduction Aimless data scaling PHASER phasing