2R4U

Crystal Structure of Wild-type E.coli GS in complex with ADP and Glucose(wtGSd)


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2QYY 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.727740%(w/v) PEG 4000, 0.2 M Na tartrate and 0.1 M HEPPSO (pH 7.7), VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
5.778.3

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 126.166α = 90
b = 126.166β = 90
c = 151.745γ = 90
Symmetry
Space GroupI 41

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCD2006-07-24MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 5ID-B1.0APS5ID-B

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
12.36797.6698.10.05911.95.1473172.7558.3
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)
2.3672.45990.5042.754.54785

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (I)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 REPLACEMENTTHROUGHOUT2QYY2.36797.132.7547142238697.660.210.1830.1820.203RANDOM41.926
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]
0.750.75-1.51
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.478
r_dihedral_angle_4_deg23.304
r_dihedral_angle_3_deg18.106
r_dihedral_angle_1_deg6.322
r_scangle_it2.184
r_scbond_it1.482
r_angle_refined_deg1.448
r_mcangle_it1.008
r_mcbond_it0.567
r_nbtor_refined0.307
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.478
r_dihedral_angle_4_deg23.304
r_dihedral_angle_3_deg18.106
r_dihedral_angle_1_deg6.322
r_scangle_it2.184
r_scbond_it1.482
r_angle_refined_deg1.448
r_mcangle_it1.008
r_mcbond_it0.567
r_nbtor_refined0.307
r_symmetry_vdw_refined0.218
r_nbd_refined0.209
r_xyhbond_nbd_refined0.144
r_symmetry_hbond_refined0.125
r_chiral_restr0.114
r_bond_refined_d0.011
r_gen_planes_refined0.005
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3735
Nucleic Acid Atoms
Solvent Atoms199
Heterogen Atoms80

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data collection