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Crystal structure of mature ThnT with a covalently bound product mimic
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3S3U PDB Entry 3S3U
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 298 15% PEG3350, 0.5M NaAcetate, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.12 42.11
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 141.543 α = 90 b = 67.324 β = 90 c = 73.792 γ = 90
Symmetry Space Group P 21 21 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 CCD RAYONIX MX-325 2009-05-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL12-2 0.80011 SSRL BL12-2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 50 99.7 0.121 5.9 6.7 47965 32.3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2 2.05 98.1 0.653 5.5 3561
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 PDB Entry 3S3U 2 30.4 47719 2358 99.08 0.1665 0.1646 0.1677 0.2021 0.2026 RANDOM 27.2127
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] -1.05 1.47 -0.42
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.907 r_dihedral_angle_4_deg 20.726 r_dihedral_angle_3_deg 13.682 r_dihedral_angle_1_deg 6.046 r_scangle_it 3.439 r_scbond_it 2.217 r_angle_refined_deg 1.504 r_mcangle_it 1.371 r_mcbond_it 0.836 r_chiral_restr 0.102
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.907 r_dihedral_angle_4_deg 20.726 r_dihedral_angle_3_deg 13.682 r_dihedral_angle_1_deg 6.046 r_scangle_it 3.439 r_scbond_it 2.217 r_angle_refined_deg 1.504 r_mcangle_it 1.371 r_mcbond_it 0.836 r_chiral_restr 0.102 r_bond_refined_d 0.016 r_gen_planes_refined 0.009
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5068 Nucleic Acid Atoms Solvent Atoms 367 Heterogen Atoms 30
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data collection HKL-2000 data reduction HKL-2000 data scaling