4MUN

Crystal structure of pantothenate synthetase in complex with 2-(5-methoxy-2-(2-nitro-4-(trifluoromethyl)phenylsulfonylcarbamoyl)-1H-indol-1-yl)acetic acid


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3LE8pdb entry 3LE8

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP829811-14% w/v PEG3000, 150 mM lithium sulfate, 100 mM imidazole, 2% v/v ethanol, 10% v/v glycerol, 20 mM magnesium chloride, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.1943.96

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 48.37α = 90
b = 70.81β = 99.15
c = 81.78γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 325 mm CCDMSINGLE 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
11.5725.2299.90.063133.72774077463418.8
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)
11.581.671000.5492.33.740175

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 3LE81.5725.1772184381699.920.165610.163780.20049RANDOM22.399
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]
0.27-0.420.94-1.08
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.342
r_dihedral_angle_4_deg20.261
r_dihedral_angle_3_deg14.251
r_long_range_B_refined7.121
r_long_range_B_other7.121
r_dihedral_angle_1_deg6.735
r_scangle_other4.642
r_scbond_it3.16
r_scbond_other3.159
r_mcangle_it3.152
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.342
r_dihedral_angle_4_deg20.261
r_dihedral_angle_3_deg14.251
r_long_range_B_refined7.121
r_long_range_B_other7.121
r_dihedral_angle_1_deg6.735
r_scangle_other4.642
r_scbond_it3.16
r_scbond_other3.159
r_mcangle_it3.152
r_mcangle_other3.15
r_angle_refined_deg2.202
r_mcbond_it2.193
r_mcbond_other2.193
r_angle_other_deg1.219
r_chiral_restr0.129
r_bond_refined_d0.023
r_gen_planes_refined0.012
r_gen_planes_other0.003
r_bond_other_d0.002
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_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4088
Nucleic Acid Atoms
Solvent Atoms491
Heterogen Atoms187

Software

Software
Software NamePurpose
MAR345dtbdata collection
AMoREphasing
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling