4V4F

The structure of the trp RNA-binding attenuation protein (TRAP) bound to a RNA molecule containing UAGAU repeats


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1C9SPDB ENTRY 1C9S

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
180.2M K-GLUTAMATE, 50 MM TRIETHANOLAMINE PH8.0, 10MM MGCL2, 8-11% MONOMETHYL ETHER PEG 2000, +0.4M KCL AT END, pH 8.00
Crystal Properties
Matthews coefficientSolvent content
4.472.02

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 113.907α = 90
b = 133.986β = 100.11
c = 232.826γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray1202002-06-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID14-2ESRFID14-2

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
11.93592.20.05619.33.3251906
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)
11.91.97580.2842.72.2

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-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 1C9S1.92024945112481000.1860.1860.236RANDOM13.53
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]
2.932.02-1.32-0.91
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg7.164
r_scangle_it6.588
r_scbond_it5.166
r_mcangle_it2.148
r_angle_refined_deg1.422
r_mcbond_it1.206
r_symmetry_vdw_refined0.242
r_symmetry_hbond_refined0.2
r_nbd_refined0.194
r_xyhbond_nbd_refined0.165
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg7.164
r_scangle_it6.588
r_scbond_it5.166
r_mcangle_it2.148
r_angle_refined_deg1.422
r_mcbond_it1.206
r_symmetry_vdw_refined0.242
r_symmetry_hbond_refined0.2
r_nbd_refined0.194
r_xyhbond_nbd_refined0.165
r_chiral_restr0.106
r_bond_refined_d0.014
r_gen_planes_refined0.006
r_bond_other_d
r_angle_other_deg
r_dihedral_angle_2_deg
r_dihedral_angle_3_deg
r_dihedral_angle_4_deg
r_gen_planes_other
r_nbd_other
r_nbtor_refined
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 Atoms11960
Nucleic Acid Atoms584
Solvent Atoms1682
Heterogen Atoms330

Software

Software
Software NamePurpose
AMoREmodel building
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing