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F2N structure, protein design with deep learning
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold AI predicted model
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6 293 25% PEG 3350, 0.15 MgOAc, 0.1 Bis TRIS pH 6.0
Crystal Properties Matthews coefficient Solvent content 2.03 39.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 47.13 α = 90 b = 48.72 β = 90 c = 75.58 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 PILATUS 6M Flat Si Rh coated M0, Kirkpatrick-Baez flat bent Si M1 & M2 2021-01-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL12-2 0.97946 SSRL BL12-2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) 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 1.58 37.79 99.9 0.05 0.051 1 32.23 33.017 24478 43.357
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.58 1.62 99.9 2.113 2.19 0.818 1.42 14.498
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 AI predicted model 1.58 37.79 23254 1224 99.91 0.1779 0.1747 0.1844 0.2379 0.2414 RANDOM 50.026
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] -0.73 -0.87 1.6
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 42.827 r_dihedral_angle_4_deg 29.361 r_dihedral_angle_3_deg 15.178 r_rigid_bond_restr 6.379 r_dihedral_angle_1_deg 5.797 r_angle_refined_deg 1.535 r_angle_other_deg 1.426 r_chiral_restr 0.07 r_bond_refined_d 0.01 r_bond_other_d 0.009
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 42.827 r_dihedral_angle_4_deg 29.361 r_dihedral_angle_3_deg 15.178 r_rigid_bond_restr 6.379 r_dihedral_angle_1_deg 5.797 r_angle_refined_deg 1.535 r_angle_other_deg 1.426 r_chiral_restr 0.07 r_bond_refined_d 0.01 r_bond_other_d 0.009 r_gen_planes_refined 0.007 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1322 Nucleic Acid Atoms Solvent Atoms 30 Heterogen Atoms
Software Software Software Name Purpose XDS data reduction XSCALE data scaling REFMAC refinement PDB_EXTRACT data extraction PHASER phasing