2CBG

Crystal structure of the PMSF-inhibited 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 MIRRORS2003-10-01MSINGLE 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
12.52491.60.0820.23.769190-341.6
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)
12.52.5654.90.224.4

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 1JMK2.524869048992.20.1660.1620.237RANDOM37.4
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]
0.530.270.53-0.8
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg8.721
r_scangle_it6.856
r_scbond_it4.495
r_mcangle_it2.982
r_angle_refined_deg2.589
r_mcbond_it1.608
r_nbd_refined0.238
r_symmetry_vdw_refined0.231
r_symmetry_hbond_refined0.231
r_xyhbond_nbd_refined0.198
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg8.721
r_scangle_it6.856
r_scbond_it4.495
r_mcangle_it2.982
r_angle_refined_deg2.589
r_mcbond_it1.608
r_nbd_refined0.238
r_symmetry_vdw_refined0.231
r_symmetry_hbond_refined0.231
r_xyhbond_nbd_refined0.198
r_chiral_restr0.167
r_bond_refined_d0.041
r_gen_planes_refined0.011
r_bond_other_d
r_angle_other_deg
r_dihedral_angle_2_deg
r_dihedral_angle_3_deg
r_dihedral_angle_4_deg
r_gen_planes_other
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_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 Atoms1665
Nucleic Acid Atoms
Solvent Atoms75
Heterogen Atoms10

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing