1PT8

Crystal structure of the yfdW gene product of E. coli, in complex with oxalate and acetyl-CoA


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1PT7Apo-form

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION6.5298PEG600, cacodylate,oxalate, acethylCoA , pH 6.5, VAPOR DIFFUSION, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
4.1770.51

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 146.786α = 90
b = 146.786β = 90
c = 129.905γ = 120
Symmetry
Space GroupP 62

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 210mirrors2003-04-09MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID290.979257ESRFID29

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
12.22098.70.1143.9479388793882
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)
12.22.3298.30.23434

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)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 REPLACEMENTTHROUGHOUTApo-form2.2207938872739664798.80.18250.182510.180560.2037RANDOM41.451
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]
-1.65-0.83-1.652.48
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg6.032
r_scangle_it4.162
r_scbond_it2.669
r_angle_refined_deg1.623
r_mcangle_it1.559
r_mcbond_it0.848
r_nbd_refined0.213
r_xyhbond_nbd_refined0.191
r_symmetry_hbond_refined0.186
r_symmetry_vdw_refined0.179
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg6.032
r_scangle_it4.162
r_scbond_it2.669
r_angle_refined_deg1.623
r_mcangle_it1.559
r_mcbond_it0.848
r_nbd_refined0.213
r_xyhbond_nbd_refined0.191
r_symmetry_hbond_refined0.186
r_symmetry_vdw_refined0.179
r_chiral_restr0.101
r_bond_refined_d0.017
r_gen_planes_refined0.007
r_bond_other_d
r_angle_other_deg
r_dihedral_angle_2_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms6440
Nucleic Acid Atoms
Solvent Atoms454
Heterogen Atoms144

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
CCP4data scaling
AMoREphasing