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Crystal structure of the Alcanivorax borkumensis YdaH transporter reveals an unusual topology
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 7.5 298 30% PEG400, 0.05M Mg(Ac)2, 0.1M NaAc(5.0), and 3% glycerol, pH 7.5, vapor diffusion, temperature 298K
Crystal Properties Matthews coefficient Solvent content 4.65 73.55
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 94.145 α = 90 b = 200.984 β = 91.82 c = 101.493 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 ACSD 2013-06-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 24-ID-C 0.98 APS 24-ID-C
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 2.96 50 96.7 0.081 8.8 1.9 74781 2 2 76.18
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 2.96 3.09 92.1 0.543 1.8
Refinement Statistics Diffraction ID Structure Solution Method 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) Mean Isotropic B X-RAY DIFFRACTION MIR 2.963 48.434 1.34 74728 74728 3766 95.7 0.2086 0.2065 0.2155 0.2502 0.2577 74.86
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 15.921 f_angle_d 1.351 f_chiral_restr 0.088 f_bond_d 0.009 f_plane_restr 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 14023 Nucleic Acid Atoms Solvent Atoms 58 Heterogen Atoms 192
Software Software Software Name Purpose SCALEPACK data scaling PHENIX refinement PDB_EXTRACT data extraction HKL-2000 data collection HKL-2000 data reduction MLPHARE phasing