1Z56

Co-Crystal Structure of Lif1p-Lig4p


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP8293Tris-HCl, Sodium Chloride, Dithiothreitol, PEG 6000, 2-(N-morpholino)ethanesulfonic acid, Ethylene Glycol, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K
Crystal Properties
Matthews coefficientSolvent content
575.1

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 247.617α = 90
b = 247.617β = 90
c = 98.416γ = 120
Symmetry
Space GroupP 64 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARRESEARCHSI-111 DOUBLE MONOCHROMATOR2004-08-20MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID13ESRFID13

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (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
13.9249.299.80.1750.1755.710.116493164752.5
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
3.923.9999.60.7990.799

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONSIRASTHROUGHOUT3.9249.2156381563883299.80.4030.40.467RANDOM107.705
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]
1.310.651.31-1.96
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg41.914
r_dihedral_angle_3_deg25.971
r_dihedral_angle_4_deg20.912
r_dihedral_angle_1_deg10.166
r_scangle_it2.151
r_angle_refined_deg2.13
r_angle_other_deg1.987
r_scbond_it1.203
r_mcangle_it1.042
r_mcbond_it0.596
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg41.914
r_dihedral_angle_3_deg25.971
r_dihedral_angle_4_deg20.912
r_dihedral_angle_1_deg10.166
r_scangle_it2.151
r_angle_refined_deg2.13
r_angle_other_deg1.987
r_scbond_it1.203
r_mcangle_it1.042
r_mcbond_it0.596
r_nbd_refined0.33
r_symmetry_vdw_refined0.325
r_nbtor_refined0.324
r_nbd_other0.323
r_xyhbond_nbd_refined0.257
r_nbtor_other0.254
r_symmetry_hbond_refined0.218
r_chiral_restr0.132
r_mcbond_other0.094
r_bond_refined_d0.016
r_bond_other_d0.012
r_gen_planes_refined0.007
r_gen_planes_other0.005
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_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4164
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALEPACKdata scaling
SHARPphasing