4HB7

The Structure of Dihydropteroate Synthase from Staphylococcus aureus subsp. aureus Mu50.


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1AD1PDB ENTRY 1AD1

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.52890.2M MgCl2, 0.1MES:NaOH pH 6.5, 10% PEG 4K, VAPOR DIFFUSION, HANGING DROP, temperature 289K
Crystal Properties
Matthews coefficientSolvent content
2.6253.01

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 90.584α = 90
b = 77.301β = 99.75
c = 90.546γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315r2011-12-11MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 19-ID0.97907APS19-ID

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
11.95088.30.053103.74267242672-323
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)
11.91.9262.90.22.21026

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 1AD11.9527.84067840678206090.430.16450.16450.16230.2056RANDOM33.391
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]
3.27-0.8-0.73-2.27
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.343
r_dihedral_angle_4_deg17.368
r_dihedral_angle_3_deg12.58
r_dihedral_angle_1_deg5.789
r_angle_refined_deg1.615
r_angle_other_deg0.835
r_chiral_restr0.097
r_bond_refined_d0.015
r_gen_planes_refined0.007
r_bond_other_d0.001
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.343
r_dihedral_angle_4_deg17.368
r_dihedral_angle_3_deg12.58
r_dihedral_angle_1_deg5.789
r_angle_refined_deg1.615
r_angle_other_deg0.835
r_chiral_restr0.097
r_bond_refined_d0.015
r_gen_planes_refined0.007
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3920
Nucleic Acid Atoms
Solvent Atoms269
Heterogen Atoms28

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
SBC-Collectdata collection
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
SHELXDphasing
SHELXEmodel building
MLPHAREphasing
DMphasing
SOLVEphasing
RESOLVEphasing
ARP/wARPmodel building
CCP4phasing
Omodel building
Cootmodel building