4FZJ

Pantothenate synthetase in complex with 1,3-DIMETHYL-1H-THIENO[2,3-C]PYRAZOLE-5-CARBOXYLIC ACID


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP829310-15% PEG3000, 150 mM Li2SO4, 0.1 M imidazole, 2% ethanol, 10% glycerol, 20 mM MgCl2, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.1943.78

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 48.29α = 90
b = 70.9β = 99.54
c = 81.83γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2012-07-02MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I030.97DiamondI03

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
11.6353.2698.20.0738.22.61766906669419
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)
11.631.7298.40.5961.82.69741

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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 REPLACEMENTTHROUGHOUT1.6353.2663290338298.080.169640.167460.2095RANDOM21.885
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]
0.6-0.40.33-1.07
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.635
r_dihedral_angle_4_deg18.508
r_dihedral_angle_3_deg14.218
r_dihedral_angle_1_deg6.17
r_scangle_it5.383
r_scbond_it3.37
r_mcangle_it2.215
r_angle_refined_deg2.133
r_mcbond_it1.355
r_chiral_restr0.155
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.635
r_dihedral_angle_4_deg18.508
r_dihedral_angle_3_deg14.218
r_dihedral_angle_1_deg6.17
r_scangle_it5.383
r_scbond_it3.37
r_mcangle_it2.215
r_angle_refined_deg2.133
r_mcbond_it1.355
r_chiral_restr0.155
r_bond_refined_d0.025
r_gen_planes_refined0.012
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_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4139
Nucleic Acid Atoms
Solvent Atoms553
Heterogen Atoms100

Software

Software
Software NamePurpose
REFMACrefinement