4KB2

Crystal structure of ribosome recycling factor mutant R109A from Mycobacterium tuberculosis


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1WQG 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1Under oil using microbatch plates7.82986% Polyethylene glycol 4000, 20mM Tris-HCl (pH 7.8), 0.6mM Cadmium acetate, 5% Polyethylene glycol 400, Under oil using microbatch plates, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.5852.28

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 56.49α = 90
b = 33.74β = 113.22
c = 61.15γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATEMAR scanner 345 mm plateOsmic mirror2011-01-23MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU RU2001.54179

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
12.356.298.60.1656.9496802233.3
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)
12.32.420.1656.949680

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 REPLACEMENTTHROUGHOUT1WQG2.351.97922744899.740.22790.226130.26686RANDOM42.023
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]
1.64-0.80.09-1.01
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg41.348
r_dihedral_angle_4_deg21.845
r_dihedral_angle_3_deg17.78
r_dihedral_angle_1_deg5.237
r_angle_refined_deg1.212
r_chiral_restr0.068
r_bond_refined_d0.01
r_gen_planes_refined0.004
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1438
Nucleic Acid Atoms
Solvent Atoms102
Heterogen Atoms3

Software

Software
Software NamePurpose
MAR345dtbdata collection
PHASERphasing
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling