2WYV

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


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
15.420% (W/V) POLYETHYLENE GLYCOL 4000, 100 MM SODIUM CITRATE PH 5.4, 2 MM NAD
Crystal Properties
Matthews coefficientSolvent content
2.244.7

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 54.27α = 90
b = 107.8β = 95.89
c = 85.98γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC CCDTOROIDAL FOCUSING MIRROR2008-07-19MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID14-4ESRFID14-4

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
11.854095.90.0610.12.97777021.5
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)
11.851.9589.20.412.22.5

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 2WYU1.8639.7576657109895.870.182770.181990.23926RANDOM22.445
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]
1.75-2.35-2.460.23
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.539
r_dihedral_angle_4_deg14.824
r_dihedral_angle_3_deg13.185
r_dihedral_angle_1_deg5.948
r_scangle_it3.791
r_scbond_it2.214
r_angle_refined_deg1.48
r_mcangle_it1.48
r_angle_other_deg1.016
r_mcbond_it0.817
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.539
r_dihedral_angle_4_deg14.824
r_dihedral_angle_3_deg13.185
r_dihedral_angle_1_deg5.948
r_scangle_it3.791
r_scbond_it2.214
r_angle_refined_deg1.48
r_mcangle_it1.48
r_angle_other_deg1.016
r_mcbond_it0.817
r_nbd_refined0.207
r_symmetry_vdw_refined0.207
r_mcbond_other0.183
r_nbd_other0.175
r_symmetry_vdw_other0.175
r_nbtor_refined0.167
r_metal_ion_refined0.154
r_xyhbond_nbd_refined0.139
r_symmetry_hbond_refined0.135
r_chiral_restr0.088
r_nbtor_other0.081
r_bond_refined_d0.016
r_gen_planes_refined0.006
r_bond_other_d0.001
r_gen_planes_other0.001
r_xyhbond_nbd_other
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 Atoms7695
Nucleic Acid Atoms
Solvent Atoms545
Heterogen Atoms91

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing