☰ Navigation Tabs
Human sigma-1 receptor bound to haloperidol
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5HK1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 LIPIDIC CUBIC PHASE 6.4 293 Protein was reconstituted in cubic phase by mixing with a 1:1.5 (w:w) protein:lipid ratio. Lipid used was a 10:1 (w:w) mix of monoolein with cholesterol. Crystals were grown in 500 mM lithium sulfate, 42% PEG 300, 1% hexanediol, 100 mM MES pH 6.4
Crystal Properties Matthews coefficient Solvent content 3.87 68.25
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 85.556 α = 90 b = 126.062 β = 90 c = 109.702 γ = 90
Symmetry Space Group P 21 21 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 80 PIXEL DECTRIS PILATUS3 6M 2016-12-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 23-ID-D 1.033 APS 23-ID-D
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 3.08 50 99.8 0.994 5.9 5.7 22196
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3.08 3.3 99.6 0.164 0.4 5
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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 MOLECULAR REPLACEMENT FREE R-VALUE 5HK1 3.084 40.509 1.33 21454 1901 93.04 0.241 0.2392 0.2406 0.2764 0.282
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 16.739 f_angle_d 0.489 f_chiral_restr 0.038 f_bond_d 0.003 f_plane_restr 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5021 Nucleic Acid Atoms Solvent Atoms 30 Heterogen Atoms 242
Software Software Software Name Purpose PHENIX refinement XDS data reduction XSCALE data scaling PHENIX phasing