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Crystal structure of Gel4 in complex with Nanobody 4
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2W62 2W62
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 291 Halogens, buffer system 3, P500MME P20K
Crystal Properties Matthews coefficient Solvent content 2.25 45.3
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 85.388 α = 90 b = 86.33 β = 90 c = 178.331 γ = 90
Symmetry Space Group P 21 21 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 S 6M 2018-12-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I24 0.97 Diamond I24
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 1.9 20.01 99.6 0.182 0.994 6 5.5 104001
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.9 2 1.588 0.537 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 (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2W62 1.9 20.01 99854 4072 99.51 0.21726 0.21537 0.2228 0.26446 0.2695 RANDOM 29.531
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] -1.34 3.39 -2.05
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.548 r_dihedral_angle_4_deg 19.776 r_dihedral_angle_3_deg 15.094 r_dihedral_angle_1_deg 7.044 r_long_range_B_refined 6.483 r_long_range_B_other 6.439 r_scangle_other 5.019 r_mcangle_other 3.321 r_mcangle_it 3.32 r_scbond_it 3.243
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.548 r_dihedral_angle_4_deg 19.776 r_dihedral_angle_3_deg 15.094 r_dihedral_angle_1_deg 7.044 r_long_range_B_refined 6.483 r_long_range_B_other 6.439 r_scangle_other 5.019 r_mcangle_other 3.321 r_mcangle_it 3.32 r_scbond_it 3.243 r_scbond_other 3.238 r_mcbond_it 2.21 r_mcbond_other 2.209 r_angle_refined_deg 1.601 r_angle_other_deg 1.334 r_chiral_restr 0.072 r_bond_refined_d 0.009 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8826 Nucleic Acid Atoms Solvent Atoms 689 Heterogen Atoms 238
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling PHASER phasing