1GTF

The structure of the trp RNA-binding attenuation protein (TRAP) bound to a 53-nucleotide RNA molecule containing GAGUU repeats


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 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
2.449

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 142.077α = 90
b = 111.493β = 117.28
c = 138.232γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray1201999-02-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID14-4ESRFID14-4

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
11.755096.10.073153546919
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)
11.751.7882.60.451.72.2

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 REPLACEMENTTHROUGHOUT1C9S1.7547.6718264318481000.1940.1940.242RANDOM
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]
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_4_deg21.025
r_dihedral_angle_3_deg14.181
r_scangle_it4.077
r_scbond_it2.862
r_mcangle_it1.698
r_angle_other_deg1.694
r_mcbond_it0.975
r_symmetry_vdw_refined0.302
r_nbd_refined0.228
r_symmetry_hbond_refined0.21
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_4_deg21.025
r_dihedral_angle_3_deg14.181
r_scangle_it4.077
r_scbond_it2.862
r_mcangle_it1.698
r_angle_other_deg1.694
r_mcbond_it0.975
r_symmetry_vdw_refined0.302
r_nbd_refined0.228
r_symmetry_hbond_refined0.21
r_xyhbond_nbd_refined0.19
r_chiral_restr0.126
r_bond_refined_d0.016
r_gen_planes_refined0.008
r_bond_other_d
r_angle_refined_deg
r_dihedral_angle_1_deg
r_dihedral_angle_2_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_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms11843
Nucleic Acid Atoms968
Solvent Atoms1466
Heterogen Atoms330

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing