2O8Q

CRYSTAL STRUCTURE OF A PROTEIN WITH A CUPIN-LIKE FOLD AND UNKNOWN FUNCTION (BXE_C0505) FROM BURKHOLDERIA XENOVORANS LB400 AT 1.55 A RESOLUTION


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP, NANODROP92772.0% Dioxane, 10.0% PEG-20000, 0.1M Bicine pH 9.0, VAPOR DIFFUSION, SITTING DROP, NANODROP, temperature 277K
2VAPOR DIFFUSION, SITTING DROP, NANODROP6.62770.2M (NH4)2Tartrate, 20.0% PEG-3350, No Buffer pH 6.6, VAPOR DIFFUSION, SITTING DROP, NANODROP, temperature 277K

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 102.255α = 90
b = 102.255β = 90
c = 74.746γ = 90
Symmetry
Space GroupP 42 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 3151m long Rh coated bent cylindrical mirror forhorizontal and vertical focussing2006-11-17MSINGLE WAVELENGTH
22x-ray100CCDMARMOSAIC 300 mm CCDAdjustable focusing mirrors in K-B geometry2006-10-20MMAD
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRL BEAMLINE BL1-5SSRLBL1-5
2SYNCHROTRONAPS BEAMLINE 23-ID-D0.97921, 0.97888, 0.94645APS23-ID-D

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
1,21.5529.6831000.0670.0677.59.15792421.35
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)
1,21.551.5999.70.9650.9650.874157

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 DIFFRACTIONMADTHROUGHOUT1.5529.68357868293999.950.1710.170.191RANDOM20.305
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]
-0.03-0.030.05
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg27.541
r_dihedral_angle_4_deg19.63
r_dihedral_angle_3_deg12.652
r_dihedral_angle_1_deg9.118
r_scangle_it6.464
r_scbond_it4.504
r_mcangle_it3.183
r_mcbond_it2.062
r_angle_refined_deg1.837
r_angle_other_deg1.006
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg27.541
r_dihedral_angle_4_deg19.63
r_dihedral_angle_3_deg12.652
r_dihedral_angle_1_deg9.118
r_scangle_it6.464
r_scbond_it4.504
r_mcangle_it3.183
r_mcbond_it2.062
r_angle_refined_deg1.837
r_angle_other_deg1.006
r_mcbond_other0.516
r_symmetry_vdw_other0.373
r_symmetry_vdw_refined0.28
r_symmetry_hbond_refined0.24
r_nbd_other0.209
r_nbd_refined0.202
r_nbtor_refined0.183
r_xyhbond_nbd_refined0.183
r_chiral_restr0.114
r_nbtor_other0.087
r_bond_refined_d0.017
r_gen_planes_refined0.008
r_bond_other_d0.002
r_gen_planes_other0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1900
Nucleic Acid Atoms
Solvent Atoms231
Heterogen Atoms34

Software

Software
Software NamePurpose
MolProbitymodel building
SHELXphasing
REFMACrefinement
SCALAdata scaling
PDB_EXTRACTdata extraction
MOSFLMdata reduction
CCP4data scaling
SHELXDphasing
SOLVEphasing