1OD8

Xylanase Xyn10A from Streptomyces lividans in complex with xylobio-isofagomine lactam


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1E0XPDB ENTRY 1E0X

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
17.520 MG/ML PROTEIN, 16% PEG 5K MME, 100 MM IMIDAZOLE, PH 7.5, 5% ISOPROPANOL
Crystal Properties
Matthews coefficientSolvent content
1.935.3

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 65.814α = 90
b = 45.878β = 90
c = 85.737γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC CCDTORROIDAL MIRROR2002-09-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID29ESRFID29

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
11.0520980.06226.44.7121638
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)
11.051.0986.40.4412.32.05

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 1E0X1.0519.8112969594597.90.1040.1030.126RANDOM8.12
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]
0.110.04-0.15
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg6.229
r_scangle_it4.558
r_scbond_it3.441
r_mcangle_it2.81
r_mcbond_it2.03
r_angle_refined_deg1.689
r_angle_other_deg0.85
r_metal_ion_refined0.614
r_nbd_other0.455
r_symmetry_vdw_other0.427
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg6.229
r_scangle_it4.558
r_scbond_it3.441
r_mcangle_it2.81
r_mcbond_it2.03
r_angle_refined_deg1.689
r_angle_other_deg0.85
r_metal_ion_refined0.614
r_nbd_other0.455
r_symmetry_vdw_other0.427
r_symmetry_vdw_refined0.382
r_metal_ion_other0.335
r_nbd_refined0.318
r_nbtor_other0.298
r_chiral_restr0.126
r_bond_refined_d0.015
r_gen_planes_refined0.004
r_bond_other_d
r_dihedral_angle_2_deg
r_dihedral_angle_3_deg
r_dihedral_angle_4_deg
r_gen_planes_other
r_nbtor_refined
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_symmetry_hbond_refined
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 Atoms2324
Nucleic Acid Atoms
Solvent Atoms629
Heterogen Atoms50

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling