3COP

Crystal Structure of E.coli GS mutant E377A in complex with ADP and acceptor analogue HEPPSO


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2QZSPDB ENTRY 2QZS

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.527740% (w/v) PEG 4000, 0.1 M HEPPSO, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 125.84α = 90
b = 125.84β = 90
c = 151.958γ = 90
Symmetry
Space GroupI 41

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray98CCDMAR CCD 165 mm2006-03-13MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 19-BM1.03APS19-BM

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
12.350930.07813.73.548231254.2
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)
2.32.494.60.42223.66111

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (I)Number Reflections (All)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 2QZS2.334.925205348150245292.560.1750.1740.197RANDOM44.487
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]
1.271.27-2.53
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg28.977
r_dihedral_angle_4_deg21.493
r_dihedral_angle_3_deg16.402
r_dihedral_angle_1_deg5.941
r_mcangle_it1.285
r_angle_refined_deg1.251
r_scangle_it0.936
r_mcbond_it0.768
r_scbond_it0.703
r_nbtor_refined0.323
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg28.977
r_dihedral_angle_4_deg21.493
r_dihedral_angle_3_deg16.402
r_dihedral_angle_1_deg5.941
r_mcangle_it1.285
r_angle_refined_deg1.251
r_scangle_it0.936
r_mcbond_it0.768
r_scbond_it0.703
r_nbtor_refined0.323
r_nbd_refined0.22
r_symmetry_hbond_refined0.203
r_symmetry_vdw_refined0.202
r_xyhbond_nbd_refined0.185
r_chiral_restr0.087
r_bond_refined_d0.009
r_gen_planes_refined0.004
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3749
Nucleic Acid Atoms
Solvent Atoms298
Heterogen Atoms56

Software

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