354D

Structure of loop E FROM E. coli 5S RRNA


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION6pH 6.00, VAPOR DIFFUSION
Crystal Properties
Matthews coefficientSolvent content
2.7254.82

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 71.184α = 90
b = 37.654β = 105.9
c = 32.944γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDPRINCETON 2KSILICON 111 BENDING MIRROR1996-09-09M
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONCHESS BEAMLINE A1CHESSA1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)R Sym 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
11.52090.70.0550.0557.14.612306-3-319.4
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.51.53540.480.482

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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 REPLACEMENTTHROUGHOUT1.52012296117090.50.2020.2020.228RANDOM24.2
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]
-5.40.72.72.8
RMS Deviations
KeyRefinement Restraint Deviation
c_dihedral_angle_d30
c_mcangle_it2.54
c_scangle_it1.9
c_mcbond_it1.79
c_scbond_it1.63
c_improper_angle_d1.42
c_angle_deg1.2
c_bond_d0.01
c_bond_d_na
c_bond_d_prot
RMS Deviations
KeyRefinement Restraint Deviation
c_dihedral_angle_d30
c_mcangle_it2.54
c_scangle_it1.9
c_mcbond_it1.79
c_scbond_it1.63
c_improper_angle_d1.42
c_angle_deg1.2
c_bond_d0.01
c_bond_d_na
c_bond_d_prot
c_angle_d
c_angle_d_na
c_angle_d_prot
c_angle_deg_na
c_angle_deg_prot
c_dihedral_angle_d_na
c_dihedral_angle_d_prot
c_improper_angle_d_na
c_improper_angle_d_prot
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms
Nucleic Acid Atoms516
Solvent Atoms124
Heterogen Atoms5

Software

Software
Software NamePurpose
X-PLORmodel building
CNSrefinement
DENZOdata reduction
X-PLORphasing