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De novo designed homodimeric NTF2-like protein with a hydrophobic pocket
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model Other computational model
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 2.5 M ammonium sulfate,
0.01 M magnesium acetate,
MES 0.05 M pH 5.6
Crystal Properties Matthews coefficient Solvent content 2.17 43.24
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 56.28 α = 90 b = 56.28 β = 90 c = 118.59 γ = 120
Symmetry Space Group P 61 2 2
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 2024-07-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALBA BEAMLINE XALOC 0.976 ALBA XALOC
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 1.5 39.53 100 1 24.4 25.6 18616
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 1.5 1.53 0.701
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 (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 1.5 37.68 17664 887 99.97 0.18576 0.18432 0.1918 0.21643 0.2207 RANDOM 32.319
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] -0.02 -0.01 -0.02 0.07
RMS Deviations Key Refinement Restraint Deviation r_long_range_B_refined 19.223 r_long_range_B_other 19.211 r_scangle_other 16.741 r_dihedral_angle_3_deg 13.574 r_dihedral_angle_1_deg 12.238 r_scbond_other 11.509 r_scbond_it 11.481 r_mcangle_other 10.33 r_mcangle_it 10.295 r_mcbond_it 7.483
RMS Deviations Key Refinement Restraint Deviation r_long_range_B_refined 19.223 r_long_range_B_other 19.211 r_scangle_other 16.741 r_dihedral_angle_3_deg 13.574 r_dihedral_angle_1_deg 12.238 r_scbond_other 11.509 r_scbond_it 11.481 r_mcangle_other 10.33 r_mcangle_it 10.295 r_mcbond_it 7.483 r_rigid_bond_restr 5.305 r_angle_refined_deg 1.706 r_angle_other_deg 0.584 r_chiral_restr 0.101 r_bond_refined_d 0.018 r_gen_planes_other 0.009 r_gen_planes_refined 0.006 r_bond_other_d r_dihedral_angle_2_deg 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_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 822 Nucleic Acid Atoms Solvent Atoms 19 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement AUTOMAR data reduction Aimless data scaling MOLREP phasing