4V8H

Crystal structure of HPF bound to the 70S ribosome.


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2WDGPDB ENTRY 2WDG and 2WDI
experimental modelPDB 2WDIPDB ENTRY 2WDG and 2WDI

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION7.62920.1-0.2M Arginine-HCl, 0.1M Tris-HCl pH 7.6, 2.5% PEG-20K, 7-12% MPD, 0.5mM BME, VAPOR DIFFUSION, temperature 292K
Crystal Properties
Matthews coefficientSolvent content
3.3157.42

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 208.97α = 90
b = 447.24β = 90
c = 617.67γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315r2011-02-06SINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSLS BEAMLINE X251.1000NSLSX25

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
13.149.985296.80.2286.015.061002309-3
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)
13.13.1892.50.0121.01

Refinement

Statistics
Diffraction IDStructure Solution MethodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (F)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTPDB ENTRY 2WDG and 2WDI3.149.9791.339931384982795.990.21780.21570.2583
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]
-8.3427-2.937311.28
RMS Deviations
KeyRefinement Restraint Deviation
f_dihedral_angle_d19.806
f_angle_d1.481
f_chiral_restr0.084
f_bond_d0.014
f_plane_restr0.009
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms18151
Nucleic Acid Atoms32270
Solvent Atoms294
Heterogen Atoms146

Software

Software
Software NamePurpose
XSCALEdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
CBASSdata collection
PHENIXmodel building
XDSdata reduction
PHENIXphasing