2Q4B

Ensemble refinement of the protein crystal structure of selenomethionyl gene product from Arabidopsis thaliana At5g02240 in space group P21212


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1YBMPDB entry 1YBM

Crystallization

Crystal Properties
Matthews coefficientSolvent content
2.549.9

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 74.634α = 90
b = 77.286β = 90
c = 92.864γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray MSINGLE 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 1YBM2.09629.08729771151992.90.180.180.257RANDOM37.8
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]
RMS Deviations
KeyRefinement Restraint Deviation
c_dihedral_angle_d23.1
c_scangle_it3.9
c_angle_deg2.9
c_mcangle_it2.66
c_scbond_it2.65
c_improper_angle_d2.19
c_mcbond_it1.71
c_bond_d0.035
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3672
Nucleic Acid Atoms
Solvent Atoms369
Heterogen Atoms96

Software

Software
Software NamePurpose
CNSrefinement
PDB_EXTRACTdata extraction
CNSphasing