3SOY

Nuclear transport factor 2 (NTF2-like) superfamily protein from Salmonella enterica subsp. enterica serovar Typhimurium str. LT2


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP72891.1M Sodium Malonate pH 7.0, 0.1M HEPES:NaOH pH 7.0, 0.5% Jeffamine ED-2001 pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 289K
Crystal Properties
Matthews coefficientSolvent content
2.5952.57

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 79.346α = 90
b = 79.346β = 90
c = 107.293γ = 90
Symmetry
Space GroupI 41 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315r2011-03-11MMAD
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 19-ID0.97931, 0.97918APS19-ID

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
1256.1195.30.0798.113.31136411364-3
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)
122.0378.30.7878.5

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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 DIFFRACTIONMADTHROUGHOUT256.11113161077953795.030.177950.175790.22085RANDOM45.72
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]
-2.64-2.645.27
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.075
r_dihedral_angle_4_deg16.115
r_dihedral_angle_3_deg14.719
r_dihedral_angle_1_deg5.417
r_scangle_it3.806
r_scbond_it2.327
r_angle_refined_deg1.742
r_mcangle_it1.361
r_angle_other_deg0.966
r_mcbond_it0.712
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.075
r_dihedral_angle_4_deg16.115
r_dihedral_angle_3_deg14.719
r_dihedral_angle_1_deg5.417
r_scangle_it3.806
r_scbond_it2.327
r_angle_refined_deg1.742
r_mcangle_it1.361
r_angle_other_deg0.966
r_mcbond_it0.712
r_mcbond_other0.192
r_chiral_restr0.096
r_bond_refined_d0.018
r_gen_planes_refined0.008
r_bond_other_d0.001
r_gen_planes_other0.001
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_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1127
Nucleic Acid Atoms
Solvent Atoms71
Heterogen Atoms18

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
MLPHAREphasing
DMphasing
REFMACrefinement
PDB_EXTRACTdata extraction
SBC-Collectdata collection
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
SHELXDphasing
SHELXEmodel building
SOLVEphasing
RESOLVEphasing
ARP/wARPmodel building
CCP4phasing
Omodel building
Cootmodel building