2YIH

Structure of a Paenibacillus polymyxa Xyloglucanase from GH family 44 with Xyloglucan


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2YKKPDB ENTRY 2YKK

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
127% (W/V) PEG 3350, 0.2 M LITHIUM SULPHATE, 0.1 M BIS TRIS PH 6.5.
Crystal Properties
Matthews coefficientSolvent content
2.755

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 83.53α = 90
b = 83.53β = 90
c = 157.14γ = 120
Symmetry
Space GroupP 31 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray120CCDADSC CCD2010-09-25MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I04DiamondI04

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
11.741.7695.80.09125.367177215.3
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)
11.71.7993.20.423.14.6

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 2YKK1.741.7663732338495.20.158180.156830.18418RANDOM14.137
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]
0.580.290.58-0.87
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.151
r_dihedral_angle_4_deg16.058
r_dihedral_angle_3_deg11.811
r_dihedral_angle_1_deg6.507
r_angle_refined_deg1.341
r_chiral_restr0.113
r_bond_refined_d0.014
r_gen_planes_refined0.012
r_bond_other_d
r_angle_other_deg
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.151
r_dihedral_angle_4_deg16.058
r_dihedral_angle_3_deg11.811
r_dihedral_angle_1_deg6.507
r_angle_refined_deg1.341
r_chiral_restr0.113
r_bond_refined_d0.014
r_gen_planes_refined0.012
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_it
r_mcbond_other
r_mcangle_it
r_mcangle_other
r_scbond_it
r_scbond_other
r_scangle_it
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 Atoms3974
Nucleic Acid Atoms
Solvent Atoms530
Heterogen Atoms113

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALAdata scaling