1ZVC

X-ray structure of allene oxide cyclase from arabidopsis thaliana AT3G25760


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1Z8K 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
16.529710 mg/ml protein, 18.4% PEG 4K, 0.160 M POTASSIUM BROMIDE, 0.100 M BISTRIS, vapor diffusion, hanging drop, temperature 297K, pH 6.50
Crystal Properties
Matthews coefficientSolvent content
2.447.9

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 66.191α = 90
b = 66.191β = 90
c = 212.7γ = 120
Symmetry
Space GroupH 3 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCDHORIZONTAL SAGITALLY FOCUSING 2ND BENT MONOCHROMATOR CRYSTAL, VERTICAL BENT FOCUSING MIRROR2005-03-12MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 22-BMAPS22-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
11.795099.50.0819.629.717352
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)
11.791.8396.70.316.2128.6

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 DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT1Z8K1.79501643787599.10.2390.2360.283RANDOM30.87
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]
-0.93-0.46-0.931.39
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg28.594
r_dihedral_angle_3_deg13.303
r_dihedral_angle_4_deg12.672
r_dihedral_angle_1_deg6.226
r_scangle_it5.498
r_scbond_it4.36
r_mcangle_it2.867
r_mcbond_it1.748
r_angle_refined_deg1.238
r_nbtor_refined0.307
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg28.594
r_dihedral_angle_3_deg13.303
r_dihedral_angle_4_deg12.672
r_dihedral_angle_1_deg6.226
r_scangle_it5.498
r_scbond_it4.36
r_mcangle_it2.867
r_mcbond_it1.748
r_angle_refined_deg1.238
r_nbtor_refined0.307
r_symmetry_hbond_refined0.203
r_nbd_refined0.198
r_symmetry_vdw_refined0.168
r_xyhbond_nbd_refined0.15
r_chiral_restr0.084
r_bond_refined_d0.011
r_gen_planes_refined0.005
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1337
Nucleic Acid Atoms
Solvent Atoms136
Heterogen Atoms1

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACTdata extraction