X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5HKE 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP4.829320% polyethylene glycol 3350, 0.2 M potassium dihydrogen phosphate pH 4.8. Then crystal is soaked in this buffer containing 5 uM glycocholic acid for 4 hrs.
Crystal Properties
Matthews coefficientSolvent content
2.2645.5

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 84.01α = 90
b = 94.09β = 90.64
c = 166.974γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRIGAKU SATURN 9442015-07-27MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU FR-E+ DW1.5418

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
12.15095.10.07312.75.314341418.4
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.12.1489.74.9

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT5HKE2.128.5135874733894.550.162680.159940.2135RANDOM27.73
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]
-2.19-1.282.58-0.36
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.223
r_dihedral_angle_3_deg14.208
r_dihedral_angle_4_deg13.151
r_dihedral_angle_1_deg6.673
r_long_range_B_refined5.719
r_long_range_B_other5.706
r_scangle_other4.247
r_mcangle_it3.374
r_mcangle_other3.374
r_scbond_it2.861
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.223
r_dihedral_angle_3_deg14.208
r_dihedral_angle_4_deg13.151
r_dihedral_angle_1_deg6.673
r_long_range_B_refined5.719
r_long_range_B_other5.706
r_scangle_other4.247
r_mcangle_it3.374
r_mcangle_other3.374
r_scbond_it2.861
r_scbond_other2.86
r_mcbond_it2.309
r_mcbond_other2.306
r_angle_refined_deg1.682
r_angle_other_deg1.015
r_chiral_restr0.103
r_bond_refined_d0.016
r_gen_planes_refined0.008
r_bond_other_d0.002
r_gen_planes_other0.002
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms20630
Nucleic Acid Atoms
Solvent Atoms989
Heterogen Atoms309

Software

Software
Software NamePurpose
REFMACrefinement
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing