3IUE

Crystal structure of pantothenate synthetase in complex with 2-(5-methoxy-2-(5-Methylpyridin-2-ylsulfonylcarbamoyl)-1H-indol-1-yl) acetic acid


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3COWPDB ENTRY 3COW

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP829312-14% PEG 3000, 100-150 mM Li2SO4, 100-150 mM imidazole, 2-4% Ethanol, 5-10% Glycerol,20 mM MgCl2, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.243.97

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 48.55α = 90
b = 70.71β = 99.37
c = 81.84γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCD2009-02-18MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X06DA0.99SLSX06DA

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
11.7327.6899.90.07911.93.75708519.5
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)
11.731.821000.5392.13.68321

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 3COW1.7327.6854175289199.930.17430.172470.20755RANDOM22.212
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]
0.42-0.580.74-1.35
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.264
r_dihedral_angle_4_deg16.251
r_dihedral_angle_3_deg14.433
r_dihedral_angle_1_deg5.771
r_scangle_it3.476
r_scbond_it2.162
r_angle_refined_deg1.49
r_mcangle_it1.455
r_mcbond_it0.91
r_nbtor_refined0.306
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.264
r_dihedral_angle_4_deg16.251
r_dihedral_angle_3_deg14.433
r_dihedral_angle_1_deg5.771
r_scangle_it3.476
r_scbond_it2.162
r_angle_refined_deg1.49
r_mcangle_it1.455
r_mcbond_it0.91
r_nbtor_refined0.306
r_symmetry_vdw_refined0.257
r_nbd_refined0.218
r_symmetry_hbond_refined0.186
r_xyhbond_nbd_refined0.152
r_chiral_restr0.092
r_bond_refined_d0.014
r_gen_planes_refined0.005
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4159
Nucleic Acid Atoms
Solvent Atoms570
Heterogen Atoms172

Software

Software
Software NamePurpose
PHASESphasing
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling