2Q14

Crystal structure of Phosphohydrolase (BT4208) from Bacteroides thetaiotaomicron VPI-5482 at 2.20 A resolution


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP8.5293NANODROP, 15.0% PEG 8000, 8.0% Ethylene glycol, 0.1M Bicine pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.957.63

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 115.436α = 90
b = 137.504β = 90
c = 279.051γ = 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 geometry2006-08-11MMAD
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 23-ID-D0.97925, 0.97939, 0.94926APS23-ID-D

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
12.249.02998.30.1645.73224828-334.1
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)
12.22.4389.30.8061.6

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 DIFFRACTIONMADTHROUGHOUT2.249.0292219711115398.750.210.2070.252RANDOM26.737
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]
1.32-1.03-0.29
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.566
r_dihedral_angle_4_deg18.2
r_dihedral_angle_3_deg15.206
r_scangle_it6.276
r_dihedral_angle_1_deg5.647
r_scbond_it4.784
r_mcangle_it2.673
r_mcbond_it1.686
r_angle_refined_deg1.416
r_angle_other_deg0.958
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.566
r_dihedral_angle_4_deg18.2
r_dihedral_angle_3_deg15.206
r_scangle_it6.276
r_dihedral_angle_1_deg5.647
r_scbond_it4.784
r_mcangle_it2.673
r_mcbond_it1.686
r_angle_refined_deg1.416
r_angle_other_deg0.958
r_mcbond_other0.383
r_nbd_refined0.219
r_nbd_other0.196
r_symmetry_vdw_other0.193
r_nbtor_refined0.183
r_symmetry_hbond_refined0.181
r_xyhbond_nbd_refined0.167
r_symmetry_vdw_refined0.142
r_nbtor_other0.088
r_chiral_restr0.082
r_xyhbond_nbd_other0.07
r_bond_refined_d0.015
r_gen_planes_refined0.005
r_bond_other_d0.002
r_gen_planes_other0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms25568
Nucleic Acid Atoms
Solvent Atoms1624
Heterogen Atoms261

Software

Software
Software NamePurpose
REFMACrefinement
PHENIXrefinement
SHELXphasing
MolProbitymodel building
XSCALEdata scaling
PDB_EXTRACTdata extraction
MAR345data collection
XDSdata reduction
SHELXDphasing
autoSHARPphasing