2UYP

Crystal structure of E. coli TdcF with bound propionate


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
2.0246.49

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 72.435α = 90
b = 85.744β = 90
c = 62.512γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATEMARRESEARCHOSMIC CONFOCAL MIRRORS2002-07-11MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU RUH3R

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
12.4525.2598.90.0812.493.41481835.93
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)
12.452.54940.32.58

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 1QU92.4424.581481775699.20.1710.1660.253RANDOM21.23
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]
-1.0070.80.207
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.278
r_dihedral_angle_4_deg22.264
r_dihedral_angle_3_deg17.594
r_dihedral_angle_1_deg7.077
r_scangle_it4.329
r_scbond_it2.766
r_angle_refined_deg1.843
r_mcangle_it1.79
r_mcbond_it1.122
r_nbtor_refined0.304
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.278
r_dihedral_angle_4_deg22.264
r_dihedral_angle_3_deg17.594
r_dihedral_angle_1_deg7.077
r_scangle_it4.329
r_scbond_it2.766
r_angle_refined_deg1.843
r_mcangle_it1.79
r_mcbond_it1.122
r_nbtor_refined0.304
r_symmetry_vdw_refined0.243
r_nbd_refined0.214
r_symmetry_hbond_refined0.206
r_xyhbond_nbd_refined0.171
r_chiral_restr0.112
r_bond_refined_d0.021
r_gen_planes_refined0.008
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 Atoms2860
Nucleic Acid Atoms
Solvent Atoms195
Heterogen Atoms10

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing