4UYK | pdb_00004uyk

Crystal structure of a Signal Recognition Particle Alu domain in the elongation arrest conformation


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1517.5% PEG 400, 5% GLYCEROL BUFFERED IN 100 MM SODIUM ACETATE PH 5.0
Crystal Properties
Matthews coefficientSolvent content
4.1273.3

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 100.86α = 90
b = 100.86β = 90
c = 197.47γ = 90
Symmetry
Space GroupP 43 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC CCD2004-04-16MMAD
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID14-1ESRFID14-1

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
13.23097.80.089.092.1830821
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
13.23.495.90.641.742.18

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-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMADTHROUGHOUTNONE3.2289.821623885499.30.193650.19160.19870.233150.2341RANDOM123.705
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]
3.443.44-6.89
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.828
r_dihedral_angle_4_deg21.631
r_dihedral_angle_3_deg19.484
r_long_range_B_refined7.091
r_long_range_B_other7.091
r_dihedral_angle_1_deg6.991
r_mcangle_it4.816
r_mcangle_other4.813
r_scangle_other4.189
r_mcbond_it2.79
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.828
r_dihedral_angle_4_deg21.631
r_dihedral_angle_3_deg19.484
r_long_range_B_refined7.091
r_long_range_B_other7.091
r_dihedral_angle_1_deg6.991
r_mcangle_it4.816
r_mcangle_other4.813
r_scangle_other4.189
r_mcbond_it2.79
r_mcbond_other2.788
r_scbond_it2.52
r_scbond_other2.519
r_angle_refined_deg1.116
r_angle_other_deg1.071
r_chiral_restr0.072
r_bond_refined_d0.005
r_gen_planes_refined0.005
r_bond_other_d0.002
r_gen_planes_other0.001
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 Atoms1377
Nucleic Acid Atoms2882
Solvent Atoms
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
SHARPphasing