1Y3T

Crystal structure of YxaG, a dioxygenase from Bacillus subtilis


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1GQGPDB Entry 1GQG

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.5298Sodium Hepes, PEG 400, Ammonium sulfate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.9357.71

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 128.417α = 90
b = 128.425β = 90
c = 51.189γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 42002-02-19MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 19-ID1APS19-ID

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
12.42098.20.08920.376.013329222
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
2.42.594.3

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (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 DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB Entry 1GQG2.491.2931547169697.540.220130.217040.27679RANDOM37.9
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]
-0.99-3.044.03
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg9.862
r_scangle_it5.693
r_scbond_it3.765
r_angle_refined_deg2.996
r_mcangle_it2.799
r_angle_other_deg2.13
r_mcbond_it1.691
r_nbd_other0.323
r_symmetry_vdw_refined0.313
r_nbd_refined0.295
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg9.862
r_scangle_it5.693
r_scbond_it3.765
r_angle_refined_deg2.996
r_mcangle_it2.799
r_angle_other_deg2.13
r_mcbond_it1.691
r_nbd_other0.323
r_symmetry_vdw_refined0.313
r_nbd_refined0.295
r_xyhbond_nbd_refined0.284
r_symmetry_vdw_other0.276
r_chiral_restr0.211
r_gen_planes_other0.162
r_nbtor_other0.145
r_bond_other_d0.13
r_gen_planes_refined0.084
r_bond_refined_d0.047
r_symmetry_hbond_refined0.023
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5141
Nucleic Acid Atoms
Solvent Atoms363
Heterogen Atoms4

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
SCALEPACKdata scaling
AMoREphasing