3SCU

Crystal Structure of Rice BGlu1 E386G Mutant Complexed with Cellopentaose


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.728822% PEG MME 5000, 0.18M ammonium sulfate, 0.1M MES, 0.002M cellopentaose, pH 6.7, VAPOR DIFFUSION, HANGING DROP, temperature 288.0K
Crystal Properties
Matthews coefficientSolvent content
2.3347.21

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 79.468α = 90
b = 100.782β = 90
c = 127.211γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray105CCDADSC QUANTUM 3152009-01-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSRRC BEAMLINE BL13B11.0NSRRCBL13B1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
11.58301000.07123.76139830
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.581.641000.4553.9613832

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 REPLACEMENTTHROUGHOUT2RGL1.5828.02132806688499.840.173850.172910.19214RANDOM13.144
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]
-0.310.68-0.37
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.83
r_dihedral_angle_4_deg21.676
r_dihedral_angle_3_deg12.049
r_dihedral_angle_1_deg5.868
r_scangle_it2.924
r_scbond_it1.818
r_angle_refined_deg1.377
r_mcangle_it1.088
r_mcbond_it0.569
r_chiral_restr0.156
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.83
r_dihedral_angle_4_deg21.676
r_dihedral_angle_3_deg12.049
r_dihedral_angle_1_deg5.868
r_scangle_it2.924
r_scbond_it1.818
r_angle_refined_deg1.377
r_mcangle_it1.088
r_mcbond_it0.569
r_chiral_restr0.156
r_bond_refined_d0.01
r_gen_planes_refined0.006
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
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_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms7608
Nucleic Acid Atoms
Solvent Atoms922
Heterogen Atoms147

Software

Software
Software NamePurpose
HKL-2000data collection
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
REFMACphasing