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Crystal structure of NeIle complexed with isoleucine
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5LTR experimental model PDB 1Z17
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 PEG 3350, Sodium acetate trihydrate
Crystal Properties Matthews coefficient Solvent content 2.45 49.78
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 63.128 α = 90 b = 68.153 β = 112.46 c = 79.479 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 RIGAKU HyPix-Arc 100 2024-02-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SEALED TUBE RIGAKU MICROMAX-003 1.5416
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 2.65 22.16 98.26 0.92 1.5 3.7 18097
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 2.65 2.72 0.65
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 2.65 22.16 17075 903 98.26 0.2387 0.23502 0.2384 0.30781 0.313 RANDOM 28.859
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] 0.86 -0.57 -0.29 -0.07
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.565 r_dihedral_angle_4_deg 25.791 r_dihedral_angle_3_deg 20.88 r_dihedral_angle_1_deg 10.499 r_long_range_B_refined 6.993 r_long_range_B_other 6.993 r_scangle_other 4.433 r_mcangle_it 4.234 r_mcangle_other 4.233 r_scbond_it 2.946
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.565 r_dihedral_angle_4_deg 25.791 r_dihedral_angle_3_deg 20.88 r_dihedral_angle_1_deg 10.499 r_long_range_B_refined 6.993 r_long_range_B_other 6.993 r_scangle_other 4.433 r_mcangle_it 4.234 r_mcangle_other 4.233 r_scbond_it 2.946 r_scbond_other 2.946 r_mcbond_it 2.83 r_mcbond_other 2.829 r_angle_refined_deg 2.275 r_angle_other_deg 1.342 r_chiral_restr 0.092 r_bond_refined_d 0.013 r_gen_planes_refined 0.01 r_gen_planes_other 0.002 r_bond_other_d 0.001 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 4353 Nucleic Acid Atoms Solvent Atoms 74 Heterogen Atoms 16
Software Software Software Name Purpose REFMAC refinement CrysalisPro data reduction Aimless data scaling MOLREP phasing