2UYN

Crystal structure of E. coli TdcF with bound 2-ketobutyrate


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1QU9PDB ENTRY 1QU9

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1710% PEG 1000, 8% PEG 8000, NO BUFFER, pH 7.00
Crystal Properties
Matthews coefficientSolvent content
2.0246.76

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 72.581α = 90
b = 85.901β = 90
c = 62.661γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC CCD2003-09-28MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID14-2ESRFID14-2

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
11.635.4294.90.0613.673.34986417.14
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)
11.61.6371.20.242.08

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 1QU91.633.48498622577950.1640.1620.204RANDOM17.75
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]
-0.7920.7050.087
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.28
r_dihedral_angle_4_deg17.065
r_dihedral_angle_3_deg13.073
r_dihedral_angle_1_deg5.628
r_scangle_it4.663
r_scbond_it3.338
r_mcangle_it1.992
r_mcbond_it1.448
r_angle_refined_deg1.441
r_nbtor_refined0.31
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.28
r_dihedral_angle_4_deg17.065
r_dihedral_angle_3_deg13.073
r_dihedral_angle_1_deg5.628
r_scangle_it4.663
r_scbond_it3.338
r_mcangle_it1.992
r_mcbond_it1.448
r_angle_refined_deg1.441
r_nbtor_refined0.31
r_nbd_refined0.212
r_symmetry_hbond_refined0.199
r_xyhbond_nbd_refined0.154
r_symmetry_vdw_refined0.148
r_chiral_restr0.098
r_bond_refined_d0.015
r_gen_planes_refined0.007
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
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 Atoms2891
Nucleic Acid Atoms
Solvent Atoms400
Heterogen Atoms21

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing