1XJ5

X-RAY STRUCTURE OF SPERMIDINE SYNTHASE FROM ARABIDOPSIS THALIANA GENE AT1G23820


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1JQ3PDB entry 1JQ3

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP629310 MG/ML PROTEIN, 24 PERCENT MEPEG 2K, 0.160 M POTASSIUM GLUTAMATE, 0.100M MES, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.4750.12

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 88.814α = 90
b = 95.207β = 104.96
c = 89.164γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray110CCDAPS-12004-07-31MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 19-BM0.97935APS19-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
12.6626.2996.80.08210.36.13968245.1
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)
2.72.7696.30.3384.15.1

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-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONSAD, MOLECULAR REPLACEMENTTHROUGHOUTPDB entry 1JQ32.726.293952937779378895.60.1880.245random43.83
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]
-3.220.3514.58-11.36
RMS Deviations
KeyRefinement Restraint Deviation
x_torsion_deg23.9
x_angle_deg1.5
x_torsion_impr_deg1.11
x_bond_d0.156
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms8868
Nucleic Acid Atoms
Solvent Atoms576
Heterogen Atoms

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RESOLVEphasing
MOLREPphasing
CNSrefinement
PHENIXphasing