2Q3U

Ensemble refinement of the protein crystal structure of gene product from Arabidopsis thaliana At5g08170, agmatine iminohydrolase


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1VKPPDB entry 1VKP

Crystallization

Crystal Properties
Matthews coefficientSolvent content
2.5551.78

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 58.02α = 90
b = 115.813β = 97.1
c = 66.634γ = 90
Symmetry
Space GroupP 1 21 1

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 1VKP1.5319.87119958603891.80.1350.1350.171RANDOM18.3
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_d24.6
c_scangle_it3.53
c_angle_deg2.7
c_scbond_it2.5
c_mcangle_it2.03
c_improper_angle_d1.97
c_mcbond_it1.41
c_bond_d0.036
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5784
Nucleic Acid Atoms
Solvent Atoms779
Heterogen Atoms67

Software

Software
Software NamePurpose
CNSrefinement
PDB_EXTRACTdata extraction
CNSphasing