2Y5J

Crystal structure of Burkholderia cenocepacia dihydropteroate synthase.


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
17.8RESERVOIR CONDITIONS 0.3 M TRIS/HCL PH8, 10% PEG 8000. PROTEIN SOLUTION BCDHPS AT 7.5 MGML-1, 2MM SULPHADOXINE, 50MM TRIS/HCL PH7.5, 250 MM NACL., pH 7.8
Crystal Properties
Matthews coefficientSolvent content
2.347

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 73.952α = 90
b = 89.433β = 90
c = 87.596γ = 90
Symmetry
Space GroupC 2 2 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 ANODE

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
12.3557.2899.50.12106.71256447.7
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)
12.352.4897.10.362.44.2

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 1AJ22.3356.991186561097.960.210630.207480.27403RANDOM39.36
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]
-1.983.06-1.08
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.475
r_dihedral_angle_4_deg18.433
r_dihedral_angle_3_deg17.499
r_dihedral_angle_1_deg7.373
r_scangle_it4.806
r_scbond_it3.334
r_angle_refined_deg2.16
r_mcangle_it2.092
r_mcbond_it1.208
r_chiral_restr0.135
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.475
r_dihedral_angle_4_deg18.433
r_dihedral_angle_3_deg17.499
r_dihedral_angle_1_deg7.373
r_scangle_it4.806
r_scbond_it3.334
r_angle_refined_deg2.16
r_mcangle_it2.092
r_mcbond_it1.208
r_chiral_restr0.135
r_gen_planes_refined0.011
r_bond_refined_d0.008
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
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_mcbond_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 Atoms1996
Nucleic Acid Atoms
Solvent Atoms89
Heterogen Atoms16

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing