4RE2

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, 0.1M Na HEPES, pH 7.25, VAPOR DIFFUSION, HANGING DROP, temperature 288K
Crystal Properties
Matthews coefficientSolvent content
2.9758.52

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 68.149α = 90
b = 71.948β = 90
c = 135.949γ = 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
123099.9457691
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
122.0799.9

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 REPLACEMENTTHROUGHOUT4JHO224.7443448225499.810.189770.187890.22543RANDOM23.793
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]
-0.220.8-0.58
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.398
r_dihedral_angle_4_deg16.725
r_dihedral_angle_3_deg14.439
r_dihedral_angle_1_deg5.69
r_scangle_it2.276
r_scbond_it1.519
r_angle_refined_deg1.155
r_mcangle_it0.985
r_mcbond_it0.595
r_nbtor_refined0.307
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.398
r_dihedral_angle_4_deg16.725
r_dihedral_angle_3_deg14.439
r_dihedral_angle_1_deg5.69
r_scangle_it2.276
r_scbond_it1.519
r_angle_refined_deg1.155
r_mcangle_it0.985
r_mcbond_it0.595
r_nbtor_refined0.307
r_nbd_refined0.189
r_symmetry_vdw_refined0.172
r_xyhbond_nbd_refined0.124
r_chiral_restr0.086
r_symmetry_hbond_refined0.072
r_bond_refined_d0.009
r_gen_planes_refined0.004
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3929
Nucleic Acid Atoms
Solvent Atoms323
Heterogen Atoms49

Software

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