1V0N

Xylanase Xyn10a from Streptomyces lividans in complex with xylobio-isofagomine at pH 7.5


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1OD8PDB ENTRY 1OD8

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
17.5100 MM IMIDAZOLE, PH 7.5 16% PEG 5K MME, 5% ISOPROPANOL
Crystal Properties
Matthews coefficientSolvent content
236.5

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 66.328α = 90
b = 46.132β = 90
c = 86.382γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC CCDTOROIDAL MIRROR2003-12-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID14-4ESRFID14-4

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
11.12395.10.05615.65.397030
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)
11.11.1670.40.2174.63

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 1OD81.122.85970305072950.1040.1030.124RANDOM8.29
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]
-0.18-0.120.31
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.855
r_dihedral_angle_4_deg15.07
r_dihedral_angle_3_deg10.613
r_dihedral_angle_1_deg6.328
r_scangle_it3.269
r_scbond_it2.643
r_mcangle_it1.999
r_angle_refined_deg1.73
r_mcbond_it1.684
r_angle_other_deg0.906
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.855
r_dihedral_angle_4_deg15.07
r_dihedral_angle_3_deg10.613
r_dihedral_angle_1_deg6.328
r_scangle_it3.269
r_scbond_it2.643
r_mcangle_it1.999
r_angle_refined_deg1.73
r_mcbond_it1.684
r_angle_other_deg0.906
r_mcbond_other0.631
r_symmetry_vdw_other0.353
r_nbd_refined0.233
r_nbd_other0.213
r_xyhbond_nbd_refined0.178
r_symmetry_hbond_refined0.157
r_symmetry_vdw_refined0.13
r_chiral_restr0.12
r_nbtor_other0.093
r_bond_refined_d0.015
r_gen_planes_refined0.01
r_bond_other_d0.001
r_gen_planes_other0.001
r_nbtor_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_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 Atoms2333
Nucleic Acid Atoms
Solvent Atoms618
Heterogen Atoms30

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling