2XGB

Crystal structure of Barley Beta-Amylase complexed with 2,3- epoxypropyl-alpha-D-glucopyranoside


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1B1YPDB ENTRY 1B1Y

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP5.5291CRYSTALS WERE GROWN AT 291 K USING THE HANGING DROP VAPOUR DIFFUSION METHOD WITH PROTEIN AT 10 MG PER ML AND A PRECIPITANT COMPRISED OF 14 PERCENT PEG 3350 IN 100 MM BIS-TRIS PROPANE BUFFER AT PH 5.5
Crystal Properties
Matthews coefficientSolvent content
1.9135.6

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 68.622α = 90
b = 71.068β = 90
c = 92.309γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCD2007-11-12MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSRS BEAMLINE PX10.1SRSPX10.1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge 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
11.1133.6996.30.13.565.98135507-910.6
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.21.2679.50.272.763.01

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 REPLACEMENTTHROUGHOUTPDB ENTRY 1B1Y1.233.168135435682395.9220.1180.11670.1407RANDOM9.8
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]
-0.2430.288-0.045
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.736
r_dihedral_angle_4_deg15.565
r_dihedral_angle_3_deg12.232
r_sphericity_free9.67
r_dihedral_angle_1_deg6.217
r_sphericity_bonded4.386
r_scangle_it4.208
r_scbond_it3.105
r_mcangle_it2.379
r_angle_refined_deg1.651
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.736
r_dihedral_angle_4_deg15.565
r_dihedral_angle_3_deg12.232
r_sphericity_free9.67
r_dihedral_angle_1_deg6.217
r_sphericity_bonded4.386
r_scangle_it4.208
r_scbond_it3.105
r_mcangle_it2.379
r_angle_refined_deg1.651
r_mcbond_it1.619
r_rigid_bond_restr1.522
r_mcbond_other0.774
r_symmetry_vdw_other0.161
r_chiral_restr0.109
r_bond_refined_d0.016
r_gen_planes_refined0.01
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_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3877
Nucleic Acid Atoms
Solvent Atoms729
Heterogen Atoms32

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing