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X-ray structure of NeIle indicator complexed with isoleucine
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1Z17
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 PEG 3350, 0.2M Sodium Acetate, pH 7.0
Crystal Properties Matthews coefficient Solvent content 2.47 50.2
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 61.1 α = 90 b = 69.2 β = 111.11 c = 80.5 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 PILATUS3 6M 2024-07-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL18U1 0.97946 SSRF BL18U1
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 1.62 75.55 100 0.99 7.5 6.7 88962
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 1.62 1.65 0.56 1.8
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 1.62 75.55 79537 3978 99.953 0.159 0.1575 0.1579 0.1837 0.1847 18.545
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] 0.274 -0.129 0.119 -0.226
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.028 r_dihedral_angle_4_deg 20.413 r_dihedral_angle_3_deg 13.184 r_dihedral_angle_1_deg 6.649 r_lrange_it 6.592 r_lrange_other 6.207 r_scangle_it 4.194 r_scangle_other 4.193 r_scbond_it 2.667 r_scbond_other 2.666
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.028 r_dihedral_angle_4_deg 20.413 r_dihedral_angle_3_deg 13.184 r_dihedral_angle_1_deg 6.649 r_lrange_it 6.592 r_lrange_other 6.207 r_scangle_it 4.194 r_scangle_other 4.193 r_scbond_it 2.667 r_scbond_other 2.666 r_mcangle_it 2.645 r_mcangle_other 2.645 r_angle_refined_deg 1.731 r_mcbond_other 1.646 r_mcbond_it 1.645 r_angle_other_deg 1.338 r_symmetry_nbd_refined 0.242 r_chiral_restr_other 0.234 r_nbd_refined 0.232 r_symmetry_xyhbond_nbd_refined 0.206 r_xyhbond_nbd_refined 0.194 r_nbd_other 0.194 r_symmetry_nbd_other 0.177 r_nbtor_refined 0.151 r_chiral_restr 0.079 r_symmetry_nbtor_other 0.077 r_bond_refined_d 0.011 r_gen_planes_refined 0.009 r_bond_other_d 0.003 r_gen_planes_other 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4370 Nucleic Acid Atoms Solvent Atoms 560 Heterogen Atoms 47
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling MOLREP phasing