6MI1

CRYSTAL STRUCTURE ANALYSIS OF THE VARIANT PLANT EXOHYDROLASE ARG158ALA-GLU161ALA IN COMPLEX WITH METHYL 6-THIO-BETA-GENTIOBIOSIDE


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1EVAPORATION727875MM 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 = 101.717α = 90
b = 101.717β = 90
c = 183.451γ = 90
Symmetry
Space GroupP 43 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 210rCOLLIMATING MIRROR2013-11-12MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAUSTRALIAN SYNCHROTRON BEAMLINE MX10.9537Australian SynchrotronMX1

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
12.388.9699.368.42841138
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.32.3699.5

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 REPLACEMENTTHROUGHOUT1IEQ2.339.1341138217599.330.169820.167510.21408RANDOM38.832
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]
0.930.93-1.87
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.301
r_dihedral_angle_4_deg20.839
r_dihedral_angle_3_deg14.628
r_dihedral_angle_1_deg7.827
r_long_range_B_other6.208
r_long_range_B_refined6.199
r_scangle_other5.149
r_scbond_it3.56
r_scbond_other3.495
r_mcangle_it3.366
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.301
r_dihedral_angle_4_deg20.839
r_dihedral_angle_3_deg14.628
r_dihedral_angle_1_deg7.827
r_long_range_B_other6.208
r_long_range_B_refined6.199
r_scangle_other5.149
r_scbond_it3.56
r_scbond_other3.495
r_mcangle_it3.366
r_mcangle_other3.366
r_mcbond_it2.367
r_mcbond_other2.366
r_angle_refined_deg1.985
r_angle_other_deg1.514
r_chiral_restr0.085
r_bond_refined_d0.014
r_gen_planes_refined0.011
r_gen_planes_other0.002
r_bond_other_d0.001
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 Atoms4586
Nucleic Acid Atoms
Solvent Atoms330
Heterogen Atoms141

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing