2PSO

Human StarD13 (DLC2) lipid transfer and protein localization domain


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP827720 % MPD, 100 mM Tris-HCl, 125 mM NaCl, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
4.0869.82

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 78.24α = 90
b = 78.24β = 90
c = 212.72γ = 90
Symmetry
Space GroupP 43

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315mirrors2006-11-30MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID14-41.03992ESRFID14-4

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym 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
12.82099.50.07316.697.5312133121386.7
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.82.91000.5543.527.63157

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB entry 1JSS2.819.792964029640157299.770.21150.21150.209730.24446RANDOM45.487
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]
0.01
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.424
r_dihedral_angle_3_deg20.139
r_dihedral_angle_4_deg18.411
r_dihedral_angle_1_deg7.333
r_mcangle_it3.943
r_scangle_it3.361
r_mcbond_it2.406
r_scbond_it2.214
r_angle_refined_deg1.454
r_nbtor_refined0.332
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.424
r_dihedral_angle_3_deg20.139
r_dihedral_angle_4_deg18.411
r_dihedral_angle_1_deg7.333
r_mcangle_it3.943
r_scangle_it3.361
r_mcbond_it2.406
r_scbond_it2.214
r_angle_refined_deg1.454
r_nbtor_refined0.332
r_nbd_refined0.198
r_symmetry_hbond_refined0.197
r_xyhbond_nbd_refined0.169
r_symmetry_vdw_refined0.15
r_chiral_restr0.096
r_bond_refined_d0.011
r_gen_planes_refined0.005
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 Atoms4477
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
ProDCdata collection
XDSdata reduction
XSCALEdata scaling
PHASERphasing
MOLREPphasing