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Inward-open structure of human glycine transporter 1 in complex with a benzoylisoindoline inhibitor and sybody Sb_GlyT1#7
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4US3 4us3, 6dzz experimental model PDB 6DZZ 4us3, 6dzz
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 LIPIDIC CUBIC PHASE 7 292.75 0.1M ADA pH 7, 13-25% PEG600, 4-14% v/v-1,3-Butanediol
Crystal Properties Matthews coefficient Solvent content 2.92 57.89
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 65.17 α = 90 b = 58.14 β = 100.38 c = 122.31 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 EIGER X 16M Mirrors 2019-10-05 M SINGLE WAVELENGTH 2 1 x-ray 100 PIXEL DECTRIS EIGER X 16M Mirrors 2019-10-04 M SINGLE WAVELENGTH 3 1 x-ray 100 PIXEL DECTRIS EIGER X 16M Mirrors 2019-09-21 M SINGLE WAVELENGTH 4 1 x-ray 100 PIXEL DECTRIS EIGER X 16M Mirrors 2019-09-19 M SINGLE WAVELENGTH 5 1 x-ray 100 PIXEL DECTRIS EIGER X 16M Mirrors 2019-08-07 M SINGLE WAVELENGTH 6 1 x-ray 100 PIXEL DECTRIS EIGER X 16M Mirrors 2019-08-06 M SINGLE WAVELENGTH 7 1 x-ray 100 PIXEL DECTRIS EIGER X 16M Mirrors 2019-07-14 M SINGLE WAVELENGTH 8 1 x-ray 100 PIXEL DECTRIS EIGER X 16M Mirrors 2019-06-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, EMBL c/o DESY BEAMLINE P14 (MX2) 0.9801 PETRA III, EMBL c/o DESY P14 (MX2) 2 SYNCHROTRON PETRA III, EMBL c/o DESY BEAMLINE P14 (MX2) 0.9801 PETRA III, EMBL c/o DESY P14 (MX2) 3 SYNCHROTRON PETRA III, EMBL c/o DESY BEAMLINE P14 (MX2) 0.9801 PETRA III, EMBL c/o DESY P14 (MX2) 4 SYNCHROTRON PETRA III, EMBL c/o DESY BEAMLINE P14 (MX2) 0.9801 PETRA III, EMBL c/o DESY P14 (MX2) 5 SYNCHROTRON PETRA III, EMBL c/o DESY BEAMLINE P14 (MX2) 0.9801 PETRA III, EMBL c/o DESY P14 (MX2) 6 SYNCHROTRON PETRA III, EMBL c/o DESY BEAMLINE P14 (MX2) 0.9801 PETRA III, EMBL c/o DESY P14 (MX2) 7 SYNCHROTRON PETRA III, EMBL c/o DESY BEAMLINE P14 (MX2) 0.9801 PETRA III, EMBL c/o DESY P14 (MX2) 8 SYNCHROTRON PETRA III, EMBL c/o DESY BEAMLINE P14 (MX2) 0.9801 PETRA III, EMBL c/o DESY P14 (MX2)
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 3.4 30 99.71 0.42 0.44 0.1225 0.985 6.57 12.1 12641 103.12
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 3.4 3.5 100 2.688 2.809 0.7956 0.541 1.69 11.9
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 4us3, 6dzz 3.4 29.67 12641 633 99.9 0.2166 0.2144 0.2368 0.2585 0.2873 RANDOM 113.5
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] -3.7653 17.4019 3.4775 0.2879
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 13.87 t_omega_torsion 4.82 t_angle_deg 1.07 t_bond_d 0.009 t_dihedral_angle_d t_trig_c_planes t_gen_planes t_it t_nbd t_improper_torsion
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 13.87 t_omega_torsion 4.82 t_angle_deg 1.07 t_bond_d 0.009 t_dihedral_angle_d t_trig_c_planes t_gen_planes t_it t_nbd t_improper_torsion t_pseud_angle t_chiral_improper_torsion t_sum_occupancies t_utility_distance t_utility_angle t_utility_torsion t_ideal_dist_contact
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5222 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 61
Software Software Software Name Purpose BUSTER refinement XDS data reduction PDB_EXTRACT data extraction XSCALE data scaling PHASER phasing