3IWJ

Crystal structure of aminoaldehyde dehydrogenase 2 from Pisum sativum (PsAMADH2)


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3IWK 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.529318% PEG 4000, 10% isopropanol, 0.5% beta-octylglucoside, 5mM NAD, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.3647.86

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 66.25α = 90
b = 86.73β = 90
c = 179.16γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 42009-04-10MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID14-20.933ESRFID14-2

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
12.153099.20.05914.757015565682142.059
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)
12.152.2699.50.4423.4

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 REPLACEMENTTHROUGHOUT3IWK2.15255371528271000.236460.233640.28935RANDOM39.288
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]
-1.454.82-3.37
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.179
r_dihedral_angle_4_deg19.634
r_dihedral_angle_3_deg16.501
r_dihedral_angle_1_deg5.298
r_scangle_it1.995
r_angle_refined_deg1.168
r_scbond_it1.143
r_mcangle_it0.722
r_mcbond_it0.372
r_chiral_restr0.074
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.179
r_dihedral_angle_4_deg19.634
r_dihedral_angle_3_deg16.501
r_dihedral_angle_1_deg5.298
r_scangle_it1.995
r_angle_refined_deg1.168
r_scbond_it1.143
r_mcangle_it0.722
r_mcbond_it0.372
r_chiral_restr0.074
r_bond_refined_d0.008
r_gen_planes_refined0.004
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
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 Atoms7622
Nucleic Acid Atoms
Solvent Atoms290
Heterogen Atoms98

Software

Software
Software NamePurpose
DNAdata collection
PHASERphasing
REFMACrefinement
XDSdata reduction
XSCALEdata scaling