1Y9A

Alcohol Dehydrogenase from Entamoeba histolotica in complex with cacodylate


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP8.5293PEG 8000 14%w/v, 300 mM Mg Acetate, 200mM cacodylate at pH 6.5, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.7754

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 76.891α = 90
b = 234.139β = 90
c = 96.241γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMAR CCD 165 mmMSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID14-1ESRFID14-1

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
11.8200.05674221
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)
11.81.8396.30.486

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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 REPLACEMENTTHROUGHOUT1.81117.0470422372292.670.128850.126250.17707RANDOM23.091
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]
-1.792.16-0.37
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.612
r_dihedral_angle_4_deg14.867
r_dihedral_angle_3_deg13.441
r_dihedral_angle_1_deg6.787
r_sphericity_free6.689
r_scangle_it6.108
r_scbond_it4.731
r_mcangle_it3.467
r_sphericity_bonded2.916
r_mcbond_it2.789
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.612
r_dihedral_angle_4_deg14.867
r_dihedral_angle_3_deg13.441
r_dihedral_angle_1_deg6.787
r_sphericity_free6.689
r_scangle_it6.108
r_scbond_it4.731
r_mcangle_it3.467
r_sphericity_bonded2.916
r_mcbond_it2.789
r_rigid_bond_restr2.212
r_angle_refined_deg1.595
r_mcbond_other1.226
r_angle_other_deg0.868
r_symmetry_vdw_other0.332
r_symmetry_hbond_refined0.304
r_symmetry_vdw_refined0.281
r_nbd_refined0.218
r_xyhbond_nbd_refined0.196
r_nbd_other0.186
r_nbtor_refined0.17
r_symmetry_metal_ion_refined0.157
r_metal_ion_refined0.15
r_chiral_restr0.099
r_nbtor_other0.085
r_xyhbond_nbd_other0.084
r_bond_refined_d0.016
r_gen_planes_refined0.006
r_bond_other_d0.001
r_gen_planes_other0.001
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_other
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5418
Nucleic Acid Atoms
Solvent Atoms754
Heterogen Atoms44

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACTdata extraction