1X38

crystal structure of barley beta-D-glucan glucohydrolase isoenzyme exo1 in complex with gluco-phenylimidazole


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1LQ2PDB ENTRY 1LQ2

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7277AMMONIUM SULPHATE, PEG 400, SODIUM ACETATE, HEPES-NAOH, pH 7.00, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
3.54247965.278549

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 100.558α = 90
b = 100.558β = 90
c = 182.414γ = 90
Symmetry
Space GroupP 43 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARRESEARCHbent cylindrical Si-mirror2004-03-29MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 14-ID-B1.127APS14-ID-B

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
11.734.399.810.05442.312.81033359815426.7
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)
11.71.7698.60.6313.4

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 1LQ21.69834.310332298154516899.810.161040.15990.159880.18301RANDOM38.787
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]
-0.39-0.390.79
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.316
r_dihedral_angle_4_deg16.085
r_dihedral_angle_3_deg12.712
r_dihedral_angle_1_deg5.9
r_scangle_it2.731
r_scbond_it1.804
r_angle_refined_deg1.326
r_mcangle_it0.986
r_mcbond_it0.638
r_nbtor_refined0.308
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.316
r_dihedral_angle_4_deg16.085
r_dihedral_angle_3_deg12.712
r_dihedral_angle_1_deg5.9
r_scangle_it2.731
r_scbond_it1.804
r_angle_refined_deg1.326
r_mcangle_it0.986
r_mcbond_it0.638
r_nbtor_refined0.308
r_symmetry_vdw_refined0.219
r_symmetry_hbond_refined0.217
r_nbd_refined0.2
r_xyhbond_nbd_refined0.127
r_chiral_restr0.095
r_bond_refined_d0.011
r_gen_planes_refined0.005
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 Atoms4566
Nucleic Acid Atoms
Solvent Atoms931
Heterogen Atoms217

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
CCP4model building
REFMACrefinement
CCP4phasing