3PG8

Truncated form of 3-deoxy-D-arabino-heptulosonate 7-phosphate synthase from Thermotoga maritima


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1RZM 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP4.6293.158%(w/v) PEG 4000, 0.1M sodium acetate, 0.02%(w/v) sodium azide, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 293.15K
Crystal Properties
Matthews coefficientSolvent content
2.0740.51

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 53.51α = 90
b = 55.456β = 90
c = 166.935γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray110CCDADSC QUANTUM 315r2010-03-03MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAUSTRALIAN SYNCHROTRON BEAMLINE MX20.9537Australian SynchrotronMX2

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
1245.04794.50.06712.33.7323853238526.42
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Rrim I (All)Rpim I (All)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
122.1196.30.2930.2930.3370.16223.74723

Refinement

Statistics
Diffraction IDStructure Solution MethodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (F)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENT1RZM238.571.3532352200693.910.1580.15460.2094Random30.2709
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]
-1.04361.3396-0.296
RMS Deviations
KeyRefinement Restraint Deviation
f_dihedral_angle_d13.467
f_angle_d0.995
f_chiral_restr0.07
f_bond_d0.006
f_plane_restr0.004
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3940
Nucleic Acid Atoms
Solvent Atoms238
Heterogen Atoms39

Software

Software
Software NamePurpose
SCALAdata processing
PHENIXrefinement
PDB_EXTRACTdata extraction
ADSCdata collection
MOSFLMdata reduction
SCALAdata scaling