2FQ1

Crystal structure of the two-domain non-ribosomal peptide synthetase EntB containing isochorismate lyase and aryl-carrier protein domains


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1NF9pdb entry 1NF9

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP827710-15% mePEG5000, 0.8M MgCl2, 10% ethylene glycol, 50mM HEPPS, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
2.6553.51

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 50.889α = 90
b = 82.331β = 90
c = 164.73γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray113IMAGE PLATERIGAKU RAXIS IVOsmic Max-Flux Confocal Mirrors2004-05-26MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU RU3001.5418

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
12.32596.30.06315.53.8311923003847.8
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)
12.32.38800.3412423

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 (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTpdb entry 1NF92.3253150929972154595.120.1890.1890.1860.241RANDOM45.001
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]
3.10.15-3.25
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.024
r_dihedral_angle_4_deg18.551
r_dihedral_angle_3_deg15.434
r_dihedral_angle_1_deg5.562
r_scangle_it5.162
r_mcangle_it4.44
r_scbond_it3.995
r_mcbond_it3.28
r_angle_refined_deg1.245
r_nbtor_refined0.3
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.024
r_dihedral_angle_4_deg18.551
r_dihedral_angle_3_deg15.434
r_dihedral_angle_1_deg5.562
r_scangle_it5.162
r_mcangle_it4.44
r_scbond_it3.995
r_mcbond_it3.28
r_angle_refined_deg1.245
r_nbtor_refined0.3
r_symmetry_hbond_refined0.227
r_nbd_refined0.189
r_xyhbond_nbd_refined0.151
r_symmetry_vdw_refined0.143
r_chiral_restr0.082
r_bond_refined_d0.011
r_gen_planes_refined0.004
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4418
Nucleic Acid Atoms
Solvent Atoms229
Heterogen Atoms14

Software

Software
Software NamePurpose
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
DENZOdata reduction
PHASERphasing