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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, 25%(w/v) PEG 3350
Crystal Properties Matthews coefficient Solvent content 3.64 66.25
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 94.96 α = 90 b = 63.723 β = 99.75 c = 219.925 γ = 90
Symmetry Space Group C 1 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 CCD RAYONIX MX225HE 2013-06-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-5A 1.0 Photon Factory BL-5A
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 3 50 92.7 0.131 5.6 3.4 24297 32.02
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 3 3.11 93.8 0.637 3.4 2370
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 4F7B 3.006 34.883 1.36 18190 894 69.56 0.2616 0.2594 0.2612 0.3044 0.3068 39.8847
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 16.375 f_angle_d 1.604 f_chiral_restr 0.057 f_bond_d 0.006 f_plane_restr 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6275 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 617
Software Software Software Name Purpose PHENIX refinement SCALEPACK data reduction PDB_EXTRACT data extraction PHASER model building SCALEPACK data scaling PHASER phasing