1XEY

Crystal structure of the complex of Escherichia coli GADA with glutarate at 2.05 A resolution


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1PMMPDB ENTRY 1PMM

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP4.6290PYRIDINE CHLORIDE, GLYCEROL,SODIUM CHLORIDE, SODIUM ACETATE, PEG 3000, pH 4.60, VAPOR DIFFUSION, HANGING DROP, temperature 290K
Crystal Properties
Matthews coefficientSolvent content
2.5852

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 117.1α = 90
b = 117.1β = 90
c = 196.4γ = 120
Symmetry
Space GroupH 3

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray293IMAGE PLATEMARRESEARCH2002-04-25MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODEELLIOTT GX-61.5418

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym 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
12.0529.2795.60.0919.97601976019711
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.052.191.10.264.46

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (F)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 1PMM2.053015336753367285789.340.1510.1510.148030.19861RANDOM23.201
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]
-0.89-0.44-0.891.33
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg5.94
r_scangle_it4.33
r_scbond_it2.64
r_mcangle_it1.588
r_angle_refined_deg1.446
r_mcbond_it0.862
r_symmetry_vdw_refined0.228
r_nbd_refined0.202
r_symmetry_hbond_refined0.157
r_xyhbond_nbd_refined0.124
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg5.94
r_scangle_it4.33
r_scbond_it2.64
r_mcangle_it1.588
r_angle_refined_deg1.446
r_mcbond_it0.862
r_symmetry_vdw_refined0.228
r_nbd_refined0.202
r_symmetry_hbond_refined0.157
r_xyhbond_nbd_refined0.124
r_chiral_restr0.1
r_bond_refined_d0.018
r_gen_planes_refined0.006
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms7107
Nucleic Acid Atoms
Solvent Atoms390
Heterogen Atoms56

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMACrefinement