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Apo crystal structure of a mutant of a computationally designed protein (TRP_F43W)
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 11.23 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 2.57 52.2
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 36.089 α = 90 b = 60.094 β = 93.6 c = 53.783 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 XE 16M 2025-02-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.9763 Diamond I04
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 1.75 53.68 99.5 0.579 13.4 3.7 23131
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 1.75 1.78 0.862 2.7
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 1.75 53.68 23006 98.97 0.2298 0.2422 0.2848 0.2996 RANDOM 27.04
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] -0.82 0.3 -1.53 2.3
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 14.627 r_dihedral_angle_2_deg 7.309 r_long_range_B_refined 6.005 r_long_range_B_other 5.783 r_dihedral_angle_1_deg 5.02 r_scangle_other 4.625 r_scbond_it 3.069 r_scbond_other 3.067 r_mcangle_other 3.047 r_mcangle_it 3.046
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 14.627 r_dihedral_angle_2_deg 7.309 r_long_range_B_refined 6.005 r_long_range_B_other 5.783 r_dihedral_angle_1_deg 5.02 r_scangle_other 4.625 r_scbond_it 3.069 r_scbond_other 3.067 r_mcangle_other 3.047 r_mcangle_it 3.046 r_mcbond_it 2.253 r_mcbond_other 2.253 r_angle_refined_deg 1.733 r_angle_other_deg 0.54 r_chiral_restr 0.078 r_bond_refined_d 0.008 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 160 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement xia2 data reduction Aimless data scaling PHASER phasing