4JHO

Structural analysis and insights into glycon specificity of the rice GH1 Os7BGlu26 beta-D-mannosidase


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2RGL 

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
2.8957.39

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 68.084α = 90
b = 71.685β = 90
c = 136.675γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray110CCDADSC QUANTUM 3152009-08-21MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSRRC BEAMLINE BL13B1NSRRCBL13B1

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
12.2125.4999.6343701
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.22.2899.9

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 REPLACEMENTTHROUGHOUT2RGL2.2125.4932558173399.590.178410.176260.21921RANDOM23.883
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]
0.17-0.18
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.177
r_dihedral_angle_4_deg19.22
r_dihedral_angle_3_deg14.453
r_dihedral_angle_1_deg5.719
r_scangle_it2.402
r_scbond_it1.709
r_angle_refined_deg1.155
r_mcangle_it0.957
r_mcbond_it0.858
r_nbtor_refined0.307
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.177
r_dihedral_angle_4_deg19.22
r_dihedral_angle_3_deg14.453
r_dihedral_angle_1_deg5.719
r_scangle_it2.402
r_scbond_it1.709
r_angle_refined_deg1.155
r_mcangle_it0.957
r_mcbond_it0.858
r_nbtor_refined0.307
r_symmetry_hbond_refined0.202
r_nbd_refined0.188
r_symmetry_vdw_refined0.163
r_xyhbond_nbd_refined0.129
r_chiral_restr0.084
r_bond_refined_d0.01
r_gen_planes_refined0.004
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3934
Nucleic Acid Atoms
Solvent Atoms304
Heterogen Atoms51

Software

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