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Crystal structure of nanoclamp8:VHH in complex with MTX
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3QXV
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6 293 15% (w/v) PEG 4000, 0.2 M DL-malate-imidazole pH 6.0, 0.1 M MgCl2
Crystal Properties Matthews coefficient Solvent content 2.63 53.21
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 54.121 α = 90 b = 95.882 β = 90 c = 118.096 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 CMOS BRUKER PHOTON 100 2020-07-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON AUSTRALIAN SYNCHROTRON BEAMLINE MX1 0.95372 Australian Synchrotron MX1
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 1.83 59.05 99.5 1 16.7 13.7 27424
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 1.83 1.88 96.5 1 13.6
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 3QXV 1.83 59.05 26016 1377 99.34 0.15205 0.14939 0.147 0.20236 0.1898 RANDOM 19.023
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] 7.29 -1.14 -6.15
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.236 r_dihedral_angle_4_deg 17.14 r_dihedral_angle_3_deg 14.321 r_sphericity_free 7.85 r_dihedral_angle_1_deg 6.792 r_scangle_it 5.405 r_scbond_it 3.874 r_sphericity_bonded 3.652 r_mcangle_it 2.781 r_rigid_bond_restr 2.645
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.236 r_dihedral_angle_4_deg 17.14 r_dihedral_angle_3_deg 14.321 r_sphericity_free 7.85 r_dihedral_angle_1_deg 6.792 r_scangle_it 5.405 r_scbond_it 3.874 r_sphericity_bonded 3.652 r_mcangle_it 2.781 r_rigid_bond_restr 2.645 r_angle_refined_deg 2.049 r_mcbond_it 1.826 r_chiral_restr 0.184 r_bond_refined_d 0.026 r_gen_planes_refined 0.012 r_bond_other_d r_angle_other_deg r_gen_planes_other 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_mcbond_other r_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2045 Nucleic Acid Atoms Solvent Atoms 390 Heterogen Atoms 35
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling PHASER phasing