1V0L

Xylanase Xyn10A from Streptomyces lividans in complex with xylobio-isofagomine at pH 5.8


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
15.820 MG/ML PROTEIN, 0.1 M MES 18% PEG 5KMME, 7.5% ISOPROPANOL, pH 5.80
Crystal Properties
Matthews coefficientSolvent content
1.935.3

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 66.018α = 90
b = 46.098β = 90
c = 86.254γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC CCDTORROIDAL MIRROR2003-09-15MSINGLE 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
10.983093.40.05826.76.7140638
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)
10.982.0289.10.4064.235.3

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 1OD80.9826.82133506699293.20.1190.1180.137RANDOM7.04
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]
-0.09-0.210.3
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg11.919
r_dihedral_angle_1_deg6.416
r_scangle_it3.365
r_scbond_it2.622
r_mcangle_it2.106
r_mcbond_it1.74
r_angle_refined_deg1.727
r_angle_other_deg0.881
r_symmetry_vdw_other0.35
r_nbd_refined0.327
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg11.919
r_dihedral_angle_1_deg6.416
r_scangle_it3.365
r_scbond_it2.622
r_mcangle_it2.106
r_mcbond_it1.74
r_angle_refined_deg1.727
r_angle_other_deg0.881
r_symmetry_vdw_other0.35
r_nbd_refined0.327
r_nbd_other0.242
r_xyhbond_nbd_refined0.163
r_symmetry_hbond_refined0.15
r_nbtor_other0.133
r_symmetry_vdw_refined0.124
r_chiral_restr0.121
r_bond_refined_d0.014
r_gen_planes_refined0.011
r_gen_planes_other0.001
r_bond_other_d
r_dihedral_angle_2_deg
r_dihedral_angle_4_deg
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_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 Atoms2331
Nucleic Acid Atoms
Solvent Atoms641
Heterogen Atoms17

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling