2CB9

Crystal structure of the thioesterase domain of the fengycin biosynthesis cluster


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1JMKPDB ENTRY 1JMK

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
15.60.2 M NH4 ACETATE; 0.1 M NA CITRATE (PH 5.6); 22.5 % PEG 8000, 10 MG/ML PROTEIN
Crystal Properties
Matthews coefficientSolvent content
2.653

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 72.354α = 90
b = 72.354β = 90
c = 96.333γ = 120
Symmetry
Space GroupP 61

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATEMARRESEARCHOSMIC MIRRORS2003-09-01MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODEENRAF-NONIUS FR591

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
11.82499.40.0632.77.826374-320.3
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)
11.81.8393.80.34.1

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 1JMK1.824.3524923133798.90.1520.150.188RANDOM17.99
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]
0.70.350.7-1.05
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg6.84
r_scangle_it5.197
r_scbond_it3.15
r_mcangle_it2.089
r_angle_refined_deg1.492
r_mcbond_it1.131
r_angle_other_deg0.839
r_symmetry_vdw_other0.307
r_symmetry_hbond_refined0.279
r_nbd_other0.249
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg6.84
r_scangle_it5.197
r_scbond_it3.15
r_mcangle_it2.089
r_angle_refined_deg1.492
r_mcbond_it1.131
r_angle_other_deg0.839
r_symmetry_vdw_other0.307
r_symmetry_hbond_refined0.279
r_nbd_other0.249
r_nbd_refined0.242
r_xyhbond_nbd_refined0.217
r_symmetry_vdw_refined0.199
r_chiral_restr0.095
r_nbtor_other0.084
r_bond_refined_d0.017
r_gen_planes_refined0.008
r_gen_planes_other0.006
r_bond_other_d0.002
r_dihedral_angle_2_deg
r_dihedral_angle_3_deg
r_dihedral_angle_4_deg
r_nbtor_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1675
Nucleic Acid Atoms
Solvent Atoms353
Heterogen Atoms4

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing