1UTD

The structure of the trp RNA-binding attenuation protein (TRAP) bound to a 63-nucleotide RNA molecule containing GAGUUU repeats


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1C9SPDB ENTYRY 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
2.1943.85

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 115.11α = 90
b = 134.23β = 106.45
c = 119.74γ = 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
12.13096.30.07915.23.399619
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)
12.12.1876.80.2543.12.2

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 ENTYRY 1C9S2.120971709861000.170.1690.228RANDOM20.31
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]
1.07-0.54-0.77-0.61
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg7.561
r_scangle_it4.465
r_scbond_it2.923
r_mcangle_it1.585
r_angle_refined_deg1.488
r_mcbond_it0.826
r_symmetry_vdw_refined0.256
r_nbd_refined0.209
r_symmetry_hbond_refined0.167
r_xyhbond_nbd_refined0.166
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg7.561
r_scangle_it4.465
r_scbond_it2.923
r_mcangle_it1.585
r_angle_refined_deg1.488
r_mcbond_it0.826
r_symmetry_vdw_refined0.256
r_nbd_refined0.209
r_symmetry_hbond_refined0.167
r_xyhbond_nbd_refined0.166
r_chiral_restr0.11
r_bond_refined_d0.015
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_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 Atoms11996
Nucleic Acid Atoms815
Solvent Atoms983
Heterogen Atoms330

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing