☰ Navigation Tabs
Crystal Structure of SCARB2 in Neural Condition (pH7.5)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4F7B
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 289 0.1 mol/L HEPES (pH 7.5),
10% v/v 2-Propanol,
20% w/v Polyethylene glycol 4000
Crystal Properties Matthews coefficient Solvent content 3.34 63.19
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 57.796 α = 90 b = 100.317 β = 98.69 c = 105.173 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 RIGAKU SATURN A200 2014-04-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL26B1 0.91998 SPring-8 BL26B1
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 2.8 50 99.1 0.105 11.6 3.7 28574 47.56
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 2.8 2.9 93.1 0.535 3.4 2674
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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 4F7B 2.889 47.154 1.36 25399 1297 95.12 0.2463 0.2438 0.2474 0.2935 0.2955 Random selection 53.3161
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 14.855 f_angle_d 1.369 f_chiral_restr 0.061 f_bond_d 0.007 f_plane_restr 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6368 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 454
Software Software Software Name Purpose PHENIX refinement SCALEPACK data reduction Coot model building PDB_EXTRACT data extraction PHASER phasing SCALEPACK data scaling