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Crystal Structure of a MES bound Substrate Binding Protein (IseP) from an Isethionate TRAP Transporter
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 293.15 0.2 M Lithium chloride, 0.1 M MES 6.0, 20 % w/v PEG 6000
Crystal Properties Matthews coefficient Solvent content 2.05 39.9
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 43.669 α = 90 b = 73.232 β = 90 c = 95.455 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 2022-11-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON AUSTRALIAN SYNCHROTRON BEAMLINE MX2 0.95372 Australian Synchrotron MX2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim 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 1.65 47.773 100 0.087 0.092 0.028 0.999 15.9 19.1 37696
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.65 1.68 1.654 1.79 0.671 0.764 13
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 NONE 1.65 47.773 37634 1908 99.992 0.199 0.1968 0.1965 0.237 0.2361 34.771
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] 3.982 -1.845 -2.137
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 16.845 r_dihedral_angle_3_deg 16.476 r_lrange_it 7.619 r_lrange_other 7.613 r_dihedral_angle_2_deg 7.212 r_scangle_it 6.593 r_scangle_other 6.591 r_dihedral_angle_1_deg 5.471 r_scbond_it 4.294 r_scbond_other 4.292
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 16.845 r_dihedral_angle_3_deg 16.476 r_lrange_it 7.619 r_lrange_other 7.613 r_dihedral_angle_2_deg 7.212 r_scangle_it 6.593 r_scangle_other 6.591 r_dihedral_angle_1_deg 5.471 r_scbond_it 4.294 r_scbond_other 4.292 r_mcangle_it 3.658 r_mcangle_other 3.657 r_mcbond_it 2.922 r_mcbond_other 2.903 r_angle_refined_deg 1.524 r_angle_other_deg 0.49 r_nbd_refined 0.218 r_nbd_other 0.191 r_symmetry_nbd_other 0.188 r_nbtor_refined 0.178 r_xyhbond_nbd_refined 0.16 r_symmetry_xyhbond_nbd_refined 0.151 r_symmetry_nbtor_other 0.079 r_symmetry_nbd_refined 0.078 r_chiral_restr 0.074 r_gen_planes_refined 0.008 r_bond_refined_d 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2405 Nucleic Acid Atoms Solvent Atoms 171 Heterogen Atoms 12
Software Software Software Name Purpose REFMAC refinement MOLREP phasing iMOSFLM data reduction Aimless data scaling