3C7E

Crystal structure of a glycoside hydrolase family 43 arabinoxylan arabinofuranohydrolase from Bacillus subtilis.


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1W9Tpdb entries 1w9t, 1gyh
experimental modelPDB 1GYHpdb entries 1w9t, 1gyh

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP52774.0 M Na formate, 30% sucrose, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
2.6152.85

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 67.71α = 90
b = 74.43β = 90
c = 106.99γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELPILATUS 6M2007-07-08MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X10SA0.9785SLSX10SA

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (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
123096.40.10210.214.14.435773
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
22.1193.20.33333.33.94.24966

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 entries 1w9t, 1gyh228.6133849188495.970.169940.167550.21333RANDOM16.75
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]
0.25-1.230.99
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.138
r_dihedral_angle_4_deg18.202
r_dihedral_angle_3_deg12.757
r_dihedral_angle_1_deg6.852
r_scangle_it2.873
r_scbond_it1.984
r_angle_refined_deg1.498
r_mcangle_it1.404
r_mcbond_it0.832
r_nbtor_refined0.305
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.138
r_dihedral_angle_4_deg18.202
r_dihedral_angle_3_deg12.757
r_dihedral_angle_1_deg6.852
r_scangle_it2.873
r_scbond_it1.984
r_angle_refined_deg1.498
r_mcangle_it1.404
r_mcbond_it0.832
r_nbtor_refined0.305
r_symmetry_vdw_refined0.214
r_nbd_refined0.208
r_symmetry_hbond_refined0.2
r_xyhbond_nbd_refined0.162
r_metal_ion_refined0.139
r_chiral_restr0.113
r_bond_refined_d0.016
r_gen_planes_refined0.006
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3671
Nucleic Acid Atoms
Solvent Atoms323
Heterogen Atoms3

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing