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Crystal structure of the human organic anion transporter MFSD10 (TETRAN)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3WDO
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 LIPIDIC CUBIC PHASE 6.5 293 0.1M ADA pH6.5 -- 0.2M lithium citrate -- 30% PEG400
Crystal Properties Matthews coefficient Solvent content 2.35 47.79
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 55.994 α = 90 b = 70.375 β = 115.45 c = 63.44 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 2018-05-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I24 0.9687 Diamond I24
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 2.4 31.74 98.7 0.208 0.234 0.104 0.99 5.7 4.9 17297 36.8
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 2.4 2.49 98.2 1.657 1.853 0.822 0.399 1 5
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 3wdo 2.4 30 16449 831 98.44 0.2112 0.2087 0.2169 0.2583 0.2618 RANDOM 36.098
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] -0.88 -1.11 0.72 0.84
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.21 r_dihedral_angle_4_deg 17.789 r_dihedral_angle_3_deg 15.631 r_dihedral_angle_1_deg 6.011 r_angle_refined_deg 1.458 r_angle_other_deg 1.252 r_chiral_restr 0.07 r_bond_refined_d 0.007 r_gen_planes_refined 0.006 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.21 r_dihedral_angle_4_deg 17.789 r_dihedral_angle_3_deg 15.631 r_dihedral_angle_1_deg 6.011 r_angle_refined_deg 1.458 r_angle_other_deg 1.252 r_chiral_restr 0.07 r_bond_refined_d 0.007 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3169 Nucleic Acid Atoms Solvent Atoms 60 Heterogen Atoms 60
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing