3GLQ

Crystal structure of S-adenosyl-L-homocysteine hydrolase from Burkholderia pseudomallei in complex with 9-beta-D-arabino-furansyl-adenine


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3D64pdb entry 3d64 split in two domains: 12-224 and 227-391

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP5.5290JCSG+ A2: 100MM NA CITRATE PH 5.5, 20% PEG 3000, BUPSA.00032.A AT 21.5MG/ML, VAPOR DIFFUSION, SITTING DROP, temperature 290K
Crystal Properties
Matthews coefficientSolvent content
2.7555.32

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 86.9α = 90
b = 86.9β = 90
c = 318.2γ = 90
Symmetry
Space GroupP 41 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRIGAKU SATIRN 944+2009-03-05MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU MICROMAX-007 HF1.5418

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
12.35095.20.08820.047.95290152901-3-327.05
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)
2.32.3680.90.5163.14.83258

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 (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTpdb entry 3d64 split in two domains: 12-224 and 227-3912.348.635282652826266695.30.1520.1520.1490.196RANDOM14.23
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]
0.730.73-1.46
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.699
r_dihedral_angle_4_deg15.788
r_dihedral_angle_3_deg13.697
r_dihedral_angle_1_deg6.293
r_scangle_it3.785
r_scbond_it2.403
r_angle_refined_deg1.643
r_mcangle_it1.401
r_angle_other_deg0.952
r_mcbond_it0.755
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.699
r_dihedral_angle_4_deg15.788
r_dihedral_angle_3_deg13.697
r_dihedral_angle_1_deg6.293
r_scangle_it3.785
r_scbond_it2.403
r_angle_refined_deg1.643
r_mcangle_it1.401
r_angle_other_deg0.952
r_mcbond_it0.755
r_mcbond_other0.188
r_chiral_restr0.096
r_bond_refined_d0.018
r_gen_planes_refined0.007
r_bond_other_d0.001
r_gen_planes_other0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms7176
Nucleic Acid Atoms
Solvent Atoms761
Heterogen Atoms126

Software

Software
Software NamePurpose
StructureStudiodata collection
PHASERphasing
REFMACrefinement
XDSdata reduction
XSCALEdata scaling