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Crystal structure of computationally designed protein VTP-4
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 0.01M NiCl2, 0.1M Tris-HCl pH8.5, 20% w/v Polyethylene glycol Monomethyl ether 2,000
Crystal Properties Matthews coefficient Solvent content 2.14 42.62
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 35.606 α = 90 b = 58.488 β = 90 c = 83.828 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 EIGER X 16M 2024-11-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL45XU 0.999990 SPring-8 BL45XU
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.6 47.97 99.9 0.085 14.9 11 23836
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.6 1.63 0.996
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-Factor (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1.6 47.967 23781 1169 99.828 0.21 0.2073 0.2188 0.2546 0.2645 24.626
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] 0.008 -0.218 0.21
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 14.136 r_dihedral_angle_3_deg 12.28 r_lrange_it 7.495 r_lrange_other 7.438 r_dihedral_angle_1_deg 6.13 r_scangle_it 5.814 r_scangle_other 5.811 r_dihedral_angle_2_deg 5.773 r_scbond_it 3.795 r_scbond_other 3.792
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 14.136 r_dihedral_angle_3_deg 12.28 r_lrange_it 7.495 r_lrange_other 7.438 r_dihedral_angle_1_deg 6.13 r_scangle_it 5.814 r_scangle_other 5.811 r_dihedral_angle_2_deg 5.773 r_scbond_it 3.795 r_scbond_other 3.792 r_mcangle_other 3.49 r_mcangle_it 3.486 r_mcbond_it 2.527 r_mcbond_other 2.527 r_angle_refined_deg 2.003 r_angle_other_deg 0.625 r_symmetry_xyhbond_nbd_refined 0.265 r_symmetry_nbd_refined 0.218 r_nbd_refined 0.213 r_symmetry_nbd_other 0.201 r_xyhbond_nbd_refined 0.2 r_nbtor_refined 0.191 r_nbd_other 0.19 r_symmetry_nbtor_other 0.089 r_chiral_restr 0.085 r_symmetry_xyhbond_nbd_other 0.084 r_bond_refined_d 0.01 r_gen_planes_refined 0.01 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1308 Nucleic Acid Atoms Solvent Atoms 135 Heterogen Atoms 28
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing