3GKJ

NPC1D(NTD):25hydroxycholesterol


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP429425% PEG 1500, 100 mM MES Acid, 30 mM Glycine, pH 4.0, VAPOR DIFFUSION, HANGING DROP, temperature 294K
Crystal Properties
Matthews coefficientSolvent content
2.0239.19

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 65.926α = 90
b = 65.926β = 90
c = 82.988γ = 120
Symmetry
Space GroupP 64

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-rayCCDADSC QUANTUM 3152008-08-09MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 19-IDAPS19-ID

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
11.65097.80.03126443
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.61.6388.3

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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 DIFFRACTIONSADTHROUGHOUT1.632.9725079132997.770.176610.175230.20295RANDOM25.431
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]
-0.37-0.18-0.370.55
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.671
r_dihedral_angle_3_deg15.373
r_dihedral_angle_4_deg11.804
r_dihedral_angle_1_deg5.776
r_scangle_it3.408
r_scbond_it2.343
r_angle_refined_deg1.476
r_mcangle_it1.345
r_mcbond_it0.823
r_nbtor_refined0.316
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.671
r_dihedral_angle_3_deg15.373
r_dihedral_angle_4_deg11.804
r_dihedral_angle_1_deg5.776
r_scangle_it3.408
r_scbond_it2.343
r_angle_refined_deg1.476
r_mcangle_it1.345
r_mcbond_it0.823
r_nbtor_refined0.316
r_symmetry_vdw_refined0.256
r_nbd_refined0.213
r_symmetry_hbond_refined0.171
r_xyhbond_nbd_refined0.106
r_chiral_restr0.099
r_bond_refined_d0.012
r_gen_planes_refined0.006
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1749
Nucleic Acid Atoms
Solvent Atoms127
Heterogen Atoms71

Software

Software
Software NamePurpose
REFMACrefinement