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Crystal Structure of SCARB2 in Acidic Condition (pH4.8)
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 0.2 mol/L ammonium sulfate, 0.1 mol/L sodium acetate trihydrate(pH 4.8), 30% w/v polyethylene glycol monomethyl ether 2000
Crystal Properties Matthews coefficient Solvent content 3.61 65.96
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 103.99 α = 90 b = 99.636 β = 90.02 c = 125.853 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 ADSC QUANTUM 210r 2013-10-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-17A 0.91998 Photon Factory BL-17A
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 3.648 50 98.4 0.141 6.5 2.9 28909 62.61
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 3.65 3.71 98.1 0.707 2.9 1408
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 3.648 48.06 1.35 23035 1166 79.71 0.2519 0.2492 0.2526 0.3035 0.3016 Random selection 60.2779
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 14.474 f_angle_d 1.281 f_chiral_restr 0.069 f_bond_d 0.006 f_plane_restr 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 12187 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 948
Software Software Software Name Purpose PHENIX refinement SCALEPACK data reduction PHASER phasing PDB_EXTRACT data extraction SCALEPACK data scaling