2WYW

High resolution structure of Thermus thermophilus enoyl-acyl carrier protein reductase NAD and triclosan-form


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2WYUPDB ENTRY 2WYU

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
15.432% (W/V) POLYETHYLENE GLYCOL 4000, 100 MM SODIUM CITRATE PH 5.4, 2 MM NAD, SOAKING FOR 48 HOURS IN 3.2 MM TRICLOSAN
Crystal Properties
Matthews coefficientSolvent content
2.140.5

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 57.71α = 90
b = 127.55β = 108.2
c = 66.5γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATEMAR555 FLAT PANELELLIPTICALLY BENT 12 QUARTZ SEGMENTS2009-07-25MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONEMBL/DESY, HAMBURG BEAMLINE X11EMBL/DESY, HAMBURGX11

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
11.93091.20.0710.53.56524421.5
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)
11.9282.10.392.93.5

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 2WYU1.927.9362991219899.920.15650.155070.19561RANDOM17.978
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]
0.83-0.31-0.61-0.41
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.359
r_dihedral_angle_4_deg17.024
r_dihedral_angle_3_deg12.13
r_dihedral_angle_1_deg6.123
r_scangle_it3.673
r_scbond_it2.146
r_angle_refined_deg1.461
r_mcangle_it1.343
r_angle_other_deg0.926
r_mcbond_it0.732
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.359
r_dihedral_angle_4_deg17.024
r_dihedral_angle_3_deg12.13
r_dihedral_angle_1_deg6.123
r_scangle_it3.673
r_scbond_it2.146
r_angle_refined_deg1.461
r_mcangle_it1.343
r_angle_other_deg0.926
r_mcbond_it0.732
r_symmetry_vdw_other0.23
r_nbd_refined0.208
r_nbd_other0.182
r_nbtor_refined0.178
r_symmetry_hbond_refined0.172
r_mcbond_other0.168
r_xyhbond_nbd_refined0.151
r_symmetry_vdw_refined0.151
r_nbtor_other0.085
r_chiral_restr0.081
r_xyhbond_nbd_other0.081
r_bond_refined_d0.014
r_gen_planes_refined0.006
r_bond_other_d0.001
r_gen_planes_other0.001
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_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 Atoms7836
Nucleic Acid Atoms
Solvent Atoms675
Heterogen Atoms244

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing