3I76

The crystal structure of the orthorhombic form of the putative HAD-hydrolase YfnB from Bacillus subtilis bound to magnesium reveals interdomain movement


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3ED5PDB entry 3ED5

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION8.5294100mM Tris HCl pH 8.5, 30% PEG 4K, 200mM magnesium chloride, vapor diffusion, temperature 294K
Crystal Properties
Matthews coefficientSolvent content
2.3547.75

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 43.685α = 90
b = 67.964β = 90
c = 271.404γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCD2009-06-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 31-ID0.97958APS31-ID

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
125091.60.0970.09733.16.7559185122120.3
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)
122.0387.70.3970.3978.96.82392

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (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 DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB entry 3ED52205585551018257391.340.1770.1750.219RANDOM23.739
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]
-0.05-1.391.44
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.352
r_dihedral_angle_4_deg22.491
r_dihedral_angle_3_deg15.072
r_dihedral_angle_1_deg5.811
r_scangle_it4.282
r_scbond_it2.73
r_mcangle_it1.707
r_angle_refined_deg1.484
r_mcbond_it0.94
r_angle_other_deg0.929
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.352
r_dihedral_angle_4_deg22.491
r_dihedral_angle_3_deg15.072
r_dihedral_angle_1_deg5.811
r_scangle_it4.282
r_scbond_it2.73
r_mcangle_it1.707
r_angle_refined_deg1.484
r_mcbond_it0.94
r_angle_other_deg0.929
r_mcbond_other0.254
r_chiral_restr0.093
r_bond_refined_d0.017
r_gen_planes_refined0.007
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5569
Nucleic Acid Atoms
Solvent Atoms405
Heterogen Atoms14

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
MAR345data collection
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing