2Q41

Ensemble refinement of the protein crystal structure of spermidine synthase from Arabidopsis thaliana gene At1g23820


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1XJ5PDB entry 1XJ5

Crystallization

Crystal Properties
Matthews coefficientSolvent content
2.4650.09

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-rayAPS-1MSINGLE WAVELENGTH

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONRe-refinement using ensemble modelTHROUGHOUTPDB entry 1XJ52.726.2937779378895.50.1640.1640.249RANDOM37.2
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]
-2.911.2414.18-11.27
RMS Deviations
KeyRefinement Restraint Deviation
c_dihedral_angle_d23.6
c_scangle_it5.02
c_mcangle_it3.87
c_scbond_it3.12
c_mcbond_it2.19
c_angle_deg1.3
c_improper_angle_d0.95
c_bond_d0.007
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms8864
Nucleic Acid Atoms
Solvent Atoms576
Heterogen Atoms

Software

Software
Software NamePurpose
CNSrefinement
PDB_EXTRACTdata extraction
CNSphasing