2QQV

Crystal structure of a cell-wall invertase (E203A) from Arabidopsis thaliana in complex with sucrose


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2AC1pdb entry 2AC1

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.52770.1M sodium cacodylate, 0.1M zinc acetate, 28% PEG 8000, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
2.7655.42

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 107.131α = 90
b = 107.131β = 90
c = 50.832γ = 120
Symmetry
Space GroupP 32

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMAR CCD 165 mm2006-05-22MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONEMBL/DESY, HAMBURG BEAMLINE X110.81620EMBL/DESY, HAMBURGX11

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
132099.42.3128181174421.41
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
133.0599.72.3

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTpdb entry 2AC13.0119.63115311174462799.260.200520.19860.23698RANDOM41.038
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]
-0.01-0.010.01
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.675
r_dihedral_angle_3_deg16.099
r_dihedral_angle_4_deg11.653
r_dihedral_angle_1_deg5.04
r_angle_refined_deg0.992
r_scangle_it0.7
r_mcangle_it0.417
r_scbond_it0.368
r_nbtor_refined0.303
r_mcbond_it0.227
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.675
r_dihedral_angle_3_deg16.099
r_dihedral_angle_4_deg11.653
r_dihedral_angle_1_deg5.04
r_angle_refined_deg0.992
r_scangle_it0.7
r_mcangle_it0.417
r_scbond_it0.368
r_nbtor_refined0.303
r_mcbond_it0.227
r_nbd_refined0.172
r_symmetry_vdw_refined0.168
r_symmetry_hbond_refined0.112
r_xyhbond_nbd_refined0.102
r_metal_ion_refined0.091
r_chiral_restr0.068
r_bond_refined_d0.006
r_gen_planes_refined0.002
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_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 Atoms4311
Nucleic Acid Atoms
Solvent Atoms14
Heterogen Atoms132

Software

Software
Software NamePurpose
MOLREPphasing
REFMACrefinement
PDB_EXTRACTdata extraction
MAR345dtbdata collection
DENZOdata reduction
SCALEPACKdata scaling