3FGY

CRYSTAL STRUCTURE OF A NTF2-LIKE PROTEIN (BXE_B1094) FROM BURKHOLDERIA XENOVORANS LB400 AT 1.59 A RESOLUTION


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP10.527730.0000% PEG-400, 0.1M CAPS pH 10.5, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
2.3146.64

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 45.95α = 90
b = 66.08β = 90
c = 91γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 300 mm CCDAdjustable focusing mirrors in K-B geometry2008-10-11MMAD
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 23-ID-B0.94645,0.97967APS23-ID-B

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
11.5929.037990.04414.924.637939-320.169
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)
11.591.6599.40.4461.7

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 DIFFRACTIONMADTHROUGHOUT1.5929.03737883189099.690.1840.1830.211RANDOM23.121
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]
0.670.09-0.76
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.782
r_dihedral_angle_4_deg15.995
r_dihedral_angle_3_deg13.872
r_dihedral_angle_1_deg5.683
r_scangle_it5.554
r_scbond_it4.22
r_mcangle_it2.62
r_mcbond_it1.952
r_angle_refined_deg1.553
r_angle_other_deg0.949
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.782
r_dihedral_angle_4_deg15.995
r_dihedral_angle_3_deg13.872
r_dihedral_angle_1_deg5.683
r_scangle_it5.554
r_scbond_it4.22
r_mcangle_it2.62
r_mcbond_it1.952
r_angle_refined_deg1.553
r_angle_other_deg0.949
r_mcbond_other0.47
r_symmetry_vdw_other0.346
r_nbd_refined0.212
r_nbd_other0.208
r_symmetry_vdw_refined0.202
r_nbtor_refined0.172
r_symmetry_hbond_refined0.155
r_xyhbond_nbd_refined0.147
r_chiral_restr0.089
r_nbtor_other0.088
r_bond_refined_d0.016
r_gen_planes_refined0.006
r_bond_other_d0.002
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2028
Nucleic Acid Atoms
Solvent Atoms329
Heterogen Atoms26

Software

Software
Software NamePurpose
REFMACrefinement
PHENIXrefinement
SHELXphasing
MolProbitymodel building
XSCALEdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction
SHELXDphasing
autoSHARPphasing