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Structure of a chimaeric beta3-alpha5 GABAA receptor in complex with nanobody Nb25
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4COF
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.8 277.15 14% poly-ethylene glycol (PEG) 5000, 0.08M magnesium acetate, 0.1M sodium citrate, 1mM ethylene glycol-bis(beta-aminoethyl ether)-N,N,N',N'-tetraacetic acid (EGTA)
Crystal Properties Matthews coefficient Solvent content 3.93 68.71
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 177.35 α = 90 b = 139.94 β = 102.25 c = 191.5 γ = 90
Symmetry Space Group C 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 2015-11-26 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) R Merge I (Observed) Rpim 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 3.3 48.88 99.78 0.352 0.116 0.998 7.85 10 68852 87.76
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3.3 3.418 99.71 2.807 0.935 0.395 1.08 9.9
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 4COF 3.3 48.88 48360 2506 73.58 0.23449 0.2337 0.2507 0.2496 0.2678 RANDOM 70.037
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] -2.2 1.92 -1.67 2.77
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.368 r_dihedral_angle_3_deg 14.586 r_dihedral_angle_4_deg 13.697 r_long_range_B_refined 8.763 r_long_range_B_other 8.763 r_dihedral_angle_1_deg 7.236 r_scangle_other 4.37 r_mcangle_it 3.682 r_mcangle_other 3.682 r_scbond_it 2.677
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.368 r_dihedral_angle_3_deg 14.586 r_dihedral_angle_4_deg 13.697 r_long_range_B_refined 8.763 r_long_range_B_other 8.763 r_dihedral_angle_1_deg 7.236 r_scangle_other 4.37 r_mcangle_it 3.682 r_mcangle_other 3.682 r_scbond_it 2.677 r_scbond_other 2.677 r_mcbond_it 2.235 r_mcbond_other 2.235 r_angle_refined_deg 0.71 r_angle_other_deg 0.501 r_chiral_restr 0.054 r_gen_planes_refined 0.012 r_bond_refined_d 0.009 r_gen_planes_other 0.003 r_bond_other_d 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 18141 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 397
Software Software Software Name Purpose HKL-2000 data reduction Aimless data scaling PHASER phasing REFMAC refinement PHENIX refinement Coot model building