2Q4D

Ensemble refinement of the crystal structure of a lysine decarboxylase-like protein from Arabidopsis thaliana gene At5g11950


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1YDHPDB entry 1YDH

Crystallization

Crystal Properties
Matthews coefficientSolvent content
2.4950.63

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 121.589α = 90
b = 80.427β = 102.97
c = 50.709γ = 90
Symmetry
Space GroupC 1 2 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 1YDH2.15234.35256781300990.1520.1520.207RANDOM26.5
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]
1.081.17-1.07
RMS Deviations
KeyRefinement Restraint Deviation
c_dihedral_angle_d21.3
c_scangle_it2.57
c_scbond_it1.96
c_mcangle_it1.73
c_mcbond_it1.2
c_angle_deg1.1
c_improper_angle_d0.83
c_bond_d0.006
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2796
Nucleic Acid Atoms
Solvent Atoms319
Heterogen Atoms20

Software

Software
Software NamePurpose
CNSrefinement
PDB_EXTRACTdata extraction
CNSphasing