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Crystal structure of the outward-facing state of the substrate-free Na+-only bound glutamate transporter homolog GltPh
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2NWW
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 LIPIDIC CUBIC PHASE 5.2 293 1M KH2PO4/Na2HPO4, pH 5.2
Crystal Properties Matthews coefficient Solvent content 4.28 71.25
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 152.011 α = 90 b = 152.011 β = 90 c = 57.521 γ = 120
Symmetry Space Group P 3 2 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 2017-07-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 0.97242 ESRF ID23-1
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 2.5 45.87 96.4 0.171 0.211 0.122 0.99 5.4 2.6 25571
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 2.5 2.6 98.5 1.365 1.684 0.968 0.25 2.6
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 2NWW 2.5 20 24338 1179 95.73 0.2133 0.2114 0.2199 0.253 0.2517 RANDOM 45.012
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] 0.27 0.14 0.27 -0.88
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.625 r_dihedral_angle_4_deg 32.454 r_dihedral_angle_3_deg 20.124 r_dihedral_angle_1_deg 6.421 r_angle_other_deg 2.098 r_angle_refined_deg 1.249 r_chiral_restr 0.064 r_bond_other_d 0.033 r_gen_planes_other 0.02 r_bond_refined_d 0.013
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.625 r_dihedral_angle_4_deg 32.454 r_dihedral_angle_3_deg 20.124 r_dihedral_angle_1_deg 6.421 r_angle_other_deg 2.098 r_angle_refined_deg 1.249 r_chiral_restr 0.064 r_bond_other_d 0.033 r_gen_planes_other 0.02 r_bond_refined_d 0.013 r_gen_planes_refined 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3019 Nucleic Acid Atoms Solvent Atoms 24 Heterogen Atoms 207
Software Software Software Name Purpose Aimless data scaling REFMAC refinement PDB_EXTRACT data extraction XDS data reduction MOLREP phasing