2X3F

Crystal Structure of the Methicillin-Resistant Staphylococcus aureus Sar2676, a Pantothenate Synthetase.


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1V8FPDB ENTRY 1V8F

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
16.510% PEG 8000, 0.1M NA MES PH6.5, 0.2M ZN ACETATE WITH 11.5MGML-1 AMP-CPP. THE CRYSTALS WERE CRYOPROTECTED WITH OIL.
Crystal Properties
Matthews coefficientSolvent content
2.245

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 45.194α = 90
b = 86.56β = 90
c = 141.573γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC CCDTOROIDAL ZERODUR MIRROR2007-10-11MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID14-2ESRFID14-2

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
11.9528.5999.60.0514.511.239073
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)
11.952980.28210.4

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 1V8F1.9528.5939073206699.610.20210.200230.23752RANDOM15.115
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]
-0.250.050.2
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.878
r_dihedral_angle_4_deg15.098
r_dihedral_angle_3_deg13.278
r_dihedral_angle_1_deg5.715
r_scangle_it2.864
r_scbond_it1.686
r_angle_refined_deg1.237
r_mcangle_it0.943
r_angle_other_deg0.825
r_mcbond_it0.514
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.878
r_dihedral_angle_4_deg15.098
r_dihedral_angle_3_deg13.278
r_dihedral_angle_1_deg5.715
r_scangle_it2.864
r_scbond_it1.686
r_angle_refined_deg1.237
r_mcangle_it0.943
r_angle_other_deg0.825
r_mcbond_it0.514
r_mcbond_other0.127
r_chiral_restr0.069
r_bond_refined_d0.01
r_gen_planes_refined0.004
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 Atoms4390
Nucleic Acid Atoms
Solvent Atoms222
Heterogen Atoms67

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing