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Crystal structure of a computationally designed protein bound to a gold cofactor (TRP_F43W.[sulfaNHC)Au])
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 9GVF
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 291 6.4 mgmL-1 TRP (in 20 mM MES pH 5.2, 150 mM NaCl) was pipetted into an MRC 3-well plate in a 1:2 ratio TRP:mother liquor, where mother liquor = 1% (w/v) tryptone, 0.05 M HEPES pH 7, 12% (w/v) PEG 3350. Crystals grew after 1-2 days.
Crystal Properties Matthews coefficient Solvent content 2.56 51.98
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 35.941 α = 90 b = 60.023 β = 92.38 c = 53.756 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 EIGER2 X 16M 2024-04-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.9763 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 2.1 53.71 97.1 0.995 10.4 1.9 13066
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 2.1 2.16 0.832 2.1
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (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 2.1 40.02 13003 96.66 0.2248 0.2363 0.2862 0.2919 RANDOM 42.96
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] 0.15 1 -1.91 1.67
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 16.213 r_long_range_B_refined 9.185 r_long_range_B_other 9.18 r_scangle_other 7.565 r_dihedral_angle_2_deg 7.266 r_mcangle_it 5.544 r_mcangle_other 5.541 r_dihedral_angle_1_deg 5.355 r_scbond_it 5.105 r_scbond_other 5.101
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 16.213 r_long_range_B_refined 9.185 r_long_range_B_other 9.18 r_scangle_other 7.565 r_dihedral_angle_2_deg 7.266 r_mcangle_it 5.544 r_mcangle_other 5.541 r_dihedral_angle_1_deg 5.355 r_scbond_it 5.105 r_scbond_other 5.101 r_mcbond_it 4.139 r_mcbond_other 4.137 r_angle_refined_deg 1.785 r_angle_other_deg 0.541 r_chiral_restr 0.073 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_dihedral_angle_4_deg 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 1556 Nucleic Acid Atoms Solvent Atoms 65 Heterogen Atoms 32
Software Software Software Name Purpose REFMAC refinement autoPROC data reduction Aimless data scaling PHASER phasing