4DDH

Pantothenate synthetase in complex with 6-methoxy-1-benzofuran-3-yl acetic acid


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP829312% 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
2.1442.45

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 48.58α = 90
b = 70.93β = 99.4
c = 82.01γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCD2008-06-17MSINGLE 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)R Sym 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
12.0753.3899.80.1230.12213.84.4148474336074
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)
12.072.181000.4994

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT3COV2.0753.383365731727169399.340.190220.187050.24987RANDOM26.386
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]
0.82-0.261.26-2.16
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.74
r_dihedral_angle_4_deg18.096
r_dihedral_angle_3_deg16.724
r_dihedral_angle_1_deg6.787
r_scangle_it4.663
r_scbond_it3.087
r_angle_refined_deg1.996
r_mcangle_it1.861
r_mcbond_it1.113
r_chiral_restr0.127
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.74
r_dihedral_angle_4_deg18.096
r_dihedral_angle_3_deg16.724
r_dihedral_angle_1_deg6.787
r_scangle_it4.663
r_scbond_it3.087
r_angle_refined_deg1.996
r_mcangle_it1.861
r_mcbond_it1.113
r_chiral_restr0.127
r_bond_refined_d0.024
r_gen_planes_refined0.01
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4174
Nucleic Acid Atoms
Solvent Atoms430
Heterogen Atoms75

Software

Software
Software NamePurpose
DNAdata collection
AMoREphasing
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling