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Crystal structure of peptide transporter POT
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other In-house Se-SAD model
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 LIPIDIC CUBIC PHASE 6.5 293 40% PEG 400, 100 mM ADA-NaOH, 160 mM Li2SO4, 4 mM SrCl2, pH 6.5, lipidic cubic phase, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.35 47.65
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 50.761 α = 90 b = 94.917 β = 111.1 c = 57.253 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 CCD RAYONIX MX225HE 2011-04-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL32XU 1.00000 SPring-8 BL32XU
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 1.9 50 88.2 0.053 15.6 2.8 35439 35439
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 1.9 1.93 72.2 0.201 1.9 1433
Refinement Statistics Diffraction ID Structure Solution Method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (All) 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 SeM-substituted protein 1.9 32.347 1.56 35267 35267 1764 88.43 0.1825 0.1808 0.1748 0.2157 0.2082 RANDOM 32.1535
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] 10.1001 0.2519 -4.0524 -6.0478
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 14.726 f_angle_d 1.053 f_chiral_restr 0.07 f_bond_d 0.007 f_plane_restr 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3720 Nucleic Acid Atoms Solvent Atoms 141 Heterogen Atoms 122
Software Software Software Name Purpose SCALEPACK data scaling PHENIX refinement PDB_EXTRACT data extraction HKL-2000 data reduction MOLREP phasing