2O2Z

Crystal structure of a protein member of the upf0052 family (bh3568) from bacillus halodurans at 2.60 A resolution


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP, NANODROP8.527740.0% polyethylene glycol 400, 0.2M lithium sulfate, 0.1M TRIS pH 8.5, VAPOR DIFFUSION, SITTING DROP, NANODROP, temperature 277K
Crystal Properties
Matthew coefficientSolvent content
3.160.27

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 51.43α = 90
b = 143.64β = 90
c = 233.68γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 3152006-08-31MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALS BEAMLINE 8.2.2ALS8.2.2

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
12.629.43799.60.08315.415438145.6
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)
2.62.6997.50.4012.9

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 DIFFRACTIONSADTHROUGHOUT2.629.43754312276499.680.190.1880.224RANDOM36.271
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]
-0.860.20.66
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.56
r_dihedral_angle_4_deg18.814
r_dihedral_angle_3_deg15.916
r_scangle_it6.797
r_dihedral_angle_1_deg5.492
r_scbond_it4.899
r_mcangle_it2.6
r_mcbond_it1.566
r_angle_refined_deg1.5
r_angle_other_deg0.92
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.56
r_dihedral_angle_4_deg18.814
r_dihedral_angle_3_deg15.916
r_scangle_it6.797
r_dihedral_angle_1_deg5.492
r_scbond_it4.899
r_mcangle_it2.6
r_mcbond_it1.566
r_angle_refined_deg1.5
r_angle_other_deg0.92
r_symmetry_vdw_refined0.342
r_mcbond_other0.238
r_nbd_refined0.216
r_nbd_other0.188
r_nbtor_refined0.175
r_symmetry_vdw_other0.174
r_xyhbond_nbd_refined0.17
r_symmetry_hbond_refined0.098
r_nbtor_other0.086
r_xyhbond_nbd_other0.081
r_chiral_restr0.072
r_bond_refined_d0.014
r_gen_planes_refined0.004
r_bond_other_d0.002
r_gen_planes_other0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms9095
Nucleic Acid Atoms
Solvent Atoms280
Heterogen Atoms216

Software

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