1GYE

Structure of Cellvibrio cellulosa alpha-L-arabinanase complexed with Arabinohexaose


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelOtherNATIVE STRUCTURE SOLVED PREVIOUSLY

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1810% PEG8000, 100MM TRIS-HCL PH8.0, 20% GLYCEROL, 100MM ARABINOTRIOSE, pH 8.00
Crystal Properties
Matthews coefficientSolvent content
2.652.2

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 90.605α = 90
b = 90.605β = 90
c = 177.554γ = 120
Symmetry
Space GroupP 65 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC CCDMSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID14-2ESRFID14-2

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
12.5201000.08230.110.4715610
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)
12.52.561000.4476.110.74

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 REPLACEMENTTHROUGHOUTNATIVE STRUCTURE SOLVED PREVIOUSLY2.520150734841000.190.1880.238RANDOM18.33
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]
2.91.452.9-4.36
RMS Deviations
KeyRefinement Restraint Deviation
r_chiral_restr7.284
r_scangle_it3.3
r_scbond_it2.249
r_angle_other_deg1.763
r_mcangle_it1.221
r_mcbond_it0.672
r_nbd_refined0.208
r_xyhbond_nbd_refined0.179
r_symmetry_vdw_refined0.155
r_symmetry_hbond_refined0.15
RMS Deviations
KeyRefinement Restraint Deviation
r_chiral_restr7.284
r_scangle_it3.3
r_scbond_it2.249
r_angle_other_deg1.763
r_mcangle_it1.221
r_mcbond_it0.672
r_nbd_refined0.208
r_xyhbond_nbd_refined0.179
r_symmetry_vdw_refined0.155
r_symmetry_hbond_refined0.15
r_bond_refined_d0.019
r_gen_planes_refined0.006
r_bond_other_d
r_angle_refined_deg
r_dihedral_angle_1_deg
r_dihedral_angle_2_deg
r_dihedral_angle_3_deg
r_dihedral_angle_4_deg
r_gen_planes_other
r_nbd_other
r_nbtor_refined
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_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2537
Nucleic Acid Atoms
Solvent Atoms77
Heterogen Atoms56

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing