3V9O

Crystal structure of Dihydroneopterin aldolase (BTH_I0291) from Burkholderia thailendensis bound to guanine.


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3O1Kpdb entry 3O1K

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP72892 M ammonium sulfate, 0.2 M lithium sulfate, 0.1 M TRIS, SSGCID: ButhA.17925.a.A1 PW33456, VAPOR DIFFUSION, SITTING DROP, temperature 289K, pH 7.0
Crystal Properties
Matthews coefficientSolvent content
2.3748.13

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 73.984α = 90
b = 73.984β = 90
c = 110.976γ = 90
Symmetry
Space GroupI 4 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315r2011-12-01MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALS BEAMLINE 5.0.10.97740ALS5.0.1

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
11.455099.90.06113.514.127570
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)
11.451.481000.55914.41351

Refinement

Statistics
Diffraction IDStructure Solution MethodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (F)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTpdb entry 3O1K1.45138.0641.342895927569139099.910.20440.17520.17360.2044Random26.1951
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]
-1.3429-1.34292.6857
RMS Deviations
KeyRefinement Restraint Deviation
f_dihedral_angle_d13.669
f_angle_d1.812
f_chiral_restr0.104
f_bond_d0.019
f_plane_restr0.01
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms945
Nucleic Acid Atoms
Solvent Atoms94
Heterogen Atoms36

Software

Software
Software NamePurpose
SCALEPACKdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
HKL-2000data collection
HKL-2000data reduction
PHASERphasing