1O03

Structure of Pentavalent Phosphorous Intermediate of an Enzyme Catalyzed Phosphoryl transfer Reaction observed on cocrystallization with Glucose 6-phosphate


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelOtherSeMeth MAD model of the same protein to 1.7 angstrom

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.929116% PEG 3350, 0.1M Ammonium Fluoride, 4mM b-D-Glucose6phosphate, pH 6.9, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties
Matthews coefficientSolvent content
1.7227.99

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 37.311α = 90
b = 54.173β = 90
c = 104.446γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray93CCDADSC QUANTUM 4mirrors2002-02-22MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 14-BM-C0.9APS14-BM-C

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (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
11.435.1496.70.10.0934.914.84121714.3
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
1.41.45880.170.1915.75

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 REPLACEMENTTHROUGHOUTSeMeth MAD model of the same protein to 1.7 angstrom1.435.144256041217416396.80.1820.220.170.194RANDOM13.7
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]
5.52-3.68-1.84
RMS Deviations
KeyRefinement Restraint Deviation
c_dihedral_angle_d21.5
c_scangle_it2.328
c_scbond_it1.66
c_mcangle_it1.301
c_angle_deg1.2
c_mcbond_it0.867
c_improper_angle_d0.82
c_bond_d0.005
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1767
Nucleic Acid Atoms
Solvent Atoms402
Heterogen Atoms21

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNSrefinement