3SCS

Crystal Structure of Rice BGlu1 E386S Mutant Complexed with alpha-Glucosyl Fluoride


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.728820% PEG MME 5000, 0.22M ammonium sulfate, 0.1M MES, 0.010M alpha-glucosyl fluoride, pH 6.7, VAPOR DIFFUSION, HANGING DROP, temperature 288.0K
Crystal Properties
Matthews coefficientSolvent content
2.3547.57

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 80.128α = 90
b = 100.86β = 90
c = 127.004γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray105CCDADSC QUANTUM 3152009-08-20MSINGLE 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
11.853099.90.12216.27.287779
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)
11.851.9299.90.4374.67.28689

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 REPLACEMENTTHROUGHOUT2RGL1.8525.383372432899.880.175330.173820.20453RANDOM10.701
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]
-0.270.89-0.63
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.038
r_dihedral_angle_4_deg20.713
r_dihedral_angle_3_deg12.139
r_dihedral_angle_1_deg5.908
r_scangle_it3.119
r_scbond_it1.914
r_angle_refined_deg1.382
r_mcangle_it1.108
r_mcbond_it0.586
r_chiral_restr0.156
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.038
r_dihedral_angle_4_deg20.713
r_dihedral_angle_3_deg12.139
r_dihedral_angle_1_deg5.908
r_scangle_it3.119
r_scbond_it1.914
r_angle_refined_deg1.382
r_mcangle_it1.108
r_mcbond_it0.586
r_chiral_restr0.156
r_bond_refined_d0.013
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 Atoms7612
Nucleic Acid Atoms
Solvent Atoms870
Heterogen Atoms71

Software

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