2Y5S

Crystal structure of Burkholderia cenocepacia dihydropteroate synthase complexed with 7,8-dihydropteroate.


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1AJ2PDB ENTRY 1AJ2

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
17.8RESERVOIR: 0.1 M TRIS/HCL PH 8, 10 % PEG 8000, 0.3 M MGCL2 PROTEIN SOLUTIONS: BCDHPS AT 7.5 MG/ML, 2 MM DIHYDROPTEROATE, 50 MM TRIS/HCL PH 7.5, 250 MM NACL.
Crystal Properties
Matthews coefficientSolvent content
2.2946.39

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 73.662α = 90
b = 86.92β = 90
c = 88.795γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray93CCDRIGAKU CCDMIRRORS2009-08-06MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU MICROMAX-007

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
11.9529.698.90.0514.44.44175027.4
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)
11.952.0693.60.373.13.7

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 1AJ21.9562.1137961202794.660.177420.175640.21114RANDOM29.049
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]
-1.35-1.412.76
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.566
r_dihedral_angle_4_deg13.637
r_dihedral_angle_3_deg13.485
r_dihedral_angle_1_deg6.002
r_scangle_it2.708
r_scbond_it1.691
r_angle_refined_deg1.232
r_mcangle_it1.052
r_angle_other_deg0.882
r_mcbond_it0.572
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.566
r_dihedral_angle_4_deg13.637
r_dihedral_angle_3_deg13.485
r_dihedral_angle_1_deg6.002
r_scangle_it2.708
r_scbond_it1.691
r_angle_refined_deg1.232
r_mcangle_it1.052
r_angle_other_deg0.882
r_mcbond_it0.572
r_mcbond_other0.128
r_chiral_restr0.073
r_bond_refined_d0.011
r_gen_planes_refined0.005
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_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4142
Nucleic Acid Atoms
Solvent Atoms305
Heterogen Atoms112

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing