4G5F

Pantothenate synthetase in complex with racemate (2S)-2,3-DIHYDRO-1,4-BENZODIOXINE-2-CARBOXYLIC ACID and (2R)-2,3-DIHYDRO-1,4-BENZODIOXINE-2-CARBOXYLIC ACID


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3COV 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP829311-14% w/v PEG3000, 150 mM lithium sulfate, 100 mM imidazole, 2% v/v ethanol, 10% v/v glycerol, 20 mM magnesium chloride, pH 8, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.1242.04

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 48.41α = 90
b = 70.99β = 99.58
c = 81.68γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100 MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X06DA0.97SLSX06DA

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
12.3347.7398.60.1137.53.6831932317931.7
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)
12.332.4690.70.4772.63.310122

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 REPLACEMENTTHROUGHOUT3COV2.3347.7321974119198.610.173820.170120.2399RANDOM31.857
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]
0.941.321.72-2.22
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.914
r_dihedral_angle_4_deg16.881
r_dihedral_angle_3_deg16.27
r_dihedral_angle_1_deg6.255
r_scangle_it4.216
r_scbond_it2.633
r_mcangle_it1.701
r_angle_refined_deg1.661
r_mcbond_it0.935
r_chiral_restr0.107
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.914
r_dihedral_angle_4_deg16.881
r_dihedral_angle_3_deg16.27
r_dihedral_angle_1_deg6.255
r_scangle_it4.216
r_scbond_it2.633
r_mcangle_it1.701
r_angle_refined_deg1.661
r_mcbond_it0.935
r_chiral_restr0.107
r_bond_refined_d0.018
r_gen_planes_refined0.009
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 Atoms4076
Nucleic Acid Atoms
Solvent Atoms216
Heterogen Atoms78

Software

Software
Software NamePurpose
REFMACrefinement