1ONI

Crystal structure of a human p14.5, a translational inhibitor reveals different mode of ligand binding near the invariant residues of the Yjgf/UK114 protein family


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7293Sodium malonate, sodium benzoate, pH 7.00, VAPOR DIFFUSION, SITTING DROP, temperature 293.0K
Crystal Properties
Matthews coefficientSolvent content
2.6753.65

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 154.158α = 90
b = 154.158β = 90
c = 104.559γ = 120
Symmetry
Space GroupP 31 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATEMARRESEARCHMIRRORS2002-12-06MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONBESSY BEAMLINE 14.2BESSY14.2

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
11.92098.40.0810.08122.96.811038529.8
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)
11.91.9294.40.550.552.3

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-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONSADTHROUGHOUT1.920110333104822551198.20.1850.216RANDOM20.6
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]
-1.24-0.62-1.241.86
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg16.46
r_dihedral_angle_1_deg15.097
r_scangle_it3.692
r_scbond_it2.24
r_mcangle_it1.627
r_angle_refined_deg1.542
r_angle_other_deg1.467
r_mcbond_it0.915
r_nbtor_other0.316
r_nbd_refined0.298
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg16.46
r_dihedral_angle_1_deg15.097
r_scangle_it3.692
r_scbond_it2.24
r_mcangle_it1.627
r_angle_refined_deg1.542
r_angle_other_deg1.467
r_mcbond_it0.915
r_nbtor_other0.316
r_nbd_refined0.298
r_symmetry_vdw_other0.242
r_nbd_other0.218
r_symmetry_hbond_refined0.21
r_symmetry_vdw_refined0.181
r_xyhbond_nbd_refined0.159
r_xyhbond_nbd_other0.121
r_chiral_restr0.094
r_bond_refined_d0.013
r_gen_planes_refined0.007
r_gen_planes_other0.005
r_bond_other_d0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms8981
Nucleic Acid Atoms
Solvent Atoms443
Heterogen Atoms117

Software

Software
Software NamePurpose
REFMACrefinement
MAR345data collection
SCALEPACKdata scaling
SnBphasing
SOLVEphasing