4RE3

Different transition state conformations for the hydrolysis of beta-mannosides and beta-glucosides in the rice Os7BGlu26 family GH1 beta-mannosidase/beta-glucosidase


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4JHO 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.252880.8M K/Na tartrate, 0.1 M HEPES, pH 7.25, VAPOR DIFFUSION, HANGING DROP, temperature 288K
Crystal Properties
Matthews coefficientSolvent content
2.9758.63

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 68.1α = 90
b = 73.209β = 90
c = 134.047γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray110CCDADSC QUANTUM 3152009-12-01MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSRRC BEAMLINE BL13B11.00NSRRCBL13B1

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
12.553099.922658226581
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.552.64100

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 REPLACEMENTTHROUGHOUT4JHO2.5524.9521454115399.90.177250.175270.21316RANDOM20.804
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]
-0.411.87-1.46
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.985
r_dihedral_angle_4_deg17.438
r_dihedral_angle_3_deg15.648
r_dihedral_angle_1_deg5.986
r_scangle_it2.704
r_scbond_it1.892
r_angle_refined_deg1.288
r_mcangle_it1.095
r_mcbond_it0.885
r_nbtor_refined0.314
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.985
r_dihedral_angle_4_deg17.438
r_dihedral_angle_3_deg15.648
r_dihedral_angle_1_deg5.986
r_scangle_it2.704
r_scbond_it1.892
r_angle_refined_deg1.288
r_mcangle_it1.095
r_mcbond_it0.885
r_nbtor_refined0.314
r_nbd_refined0.204
r_symmetry_hbond_refined0.161
r_symmetry_vdw_refined0.148
r_xyhbond_nbd_refined0.129
r_chiral_restr0.097
r_bond_refined_d0.011
r_gen_planes_refined0.005
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3934
Nucleic Acid Atoms
Solvent Atoms119
Heterogen Atoms61

Software

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