6MD6

CRYSTAL STRUCTURE ANALYSIS OF PLANT EXOHYDROLASE IN COMPLEX WITH METHYL 2-THIO-BETA-SOPHOROSIDE


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP727775MM HEPES-NAOH PH7.0, 1.2% PEG 400, 1.7M AMMONIUM SULPHATE , VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 277K
Crystal Properties
Matthews coefficientSolvent content
3.6366.13

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 100.311α = 90
b = 100.311β = 90
c = 182.153γ = 90
Symmetry
Space GroupP 43 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 210rCOLLIMATING MIRROR2012-11-22MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAUSTRALIAN SYNCHROTRON BEAMLINE MX10.9537Australian SynchrotronMX1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)R Sym 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
11.6848.3699.70.0760.07439.1929.21011192
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.681.7899.30.760.75428

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 REPLACEMENTTHROUGHOUT1IEQ1.6846.13101119531199.910.133470.13210.15902RANDOM21.527
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]
-0.02-0.020.03
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.549
r_dihedral_angle_4_deg17.169
r_dihedral_angle_3_deg12.974
r_long_range_B_refined7.425
r_dihedral_angle_1_deg6.915
r_long_range_B_other6.858
r_scangle_other4.013
r_scbond_it2.843
r_scbond_other2.843
r_angle_refined_deg2.282
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.549
r_dihedral_angle_4_deg17.169
r_dihedral_angle_3_deg12.974
r_long_range_B_refined7.425
r_dihedral_angle_1_deg6.915
r_long_range_B_other6.858
r_scangle_other4.013
r_scbond_it2.843
r_scbond_other2.843
r_angle_refined_deg2.282
r_angle_other_deg1.907
r_mcangle_it1.891
r_mcangle_other1.891
r_mcbond_it1.28
r_mcbond_other1.28
r_chiral_restr0.126
r_bond_refined_d0.02
r_gen_planes_refined0.014
r_bond_other_d0.001
r_gen_planes_other0.001
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_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4576
Nucleic Acid Atoms
Solvent Atoms1003
Heterogen Atoms172

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing