3TM5

Crystal structure of Trm14 from Pyrococcus furiosus in complex with sinefungin


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP8293100 mM Tris-acetate, 32% PEG 4000, 15% glycerol, crystal was soaked in crystallization solution containing 1 mM sinefungin, pH 8, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.6653.79

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 82.245α = 90
b = 45.064β = 91.81
c = 121.082γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCD2011-02-05MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X06DA0.98000SLSX06DA

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
12.275098.70.1478.63.88067655944
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)
12.272.492.80.6432.083.7

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)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 3TLJ2.2748.024317536169190890.990.204740.203970.21892RANDOM24.383
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]
9.151.85-6.02-3.12
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.082
r_dihedral_angle_4_deg20.601
r_dihedral_angle_3_deg17.771
r_dihedral_angle_1_deg7.904
r_scangle_it5.28
r_scbond_it3.483
r_mcangle_it2.113
r_angle_refined_deg1.61
r_mcbond_it1.23
r_chiral_restr0.111
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.082
r_dihedral_angle_4_deg20.601
r_dihedral_angle_3_deg17.771
r_dihedral_angle_1_deg7.904
r_scangle_it5.28
r_scbond_it3.483
r_mcangle_it2.113
r_angle_refined_deg1.61
r_mcbond_it1.23
r_chiral_restr0.111
r_bond_refined_d0.014
r_gen_planes_refined0.011
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
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 Atoms5835
Nucleic Acid Atoms
Solvent Atoms253
Heterogen Atoms54

Software

Software
Software NamePurpose
XDSdata scaling
PHASERphasing
REFMACrefinement
XDSdata reduction