1V0M

Xylanase Xyn10a from Streptomyces lividans in complex with xylobio-deoxynojirimycin 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 = 66.884α = 90
b = 46.081β = 90
c = 85.789γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC CCDSAGITALLY FOCUSING GE(220) AND A MULTILAYER2002-09-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID14-1ESRFID14-1

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
11.072094.40.06325.545.7117436
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)
11.071.1181.20.4662.945.93

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 1OD81.0719.65105254553094.40.0990.0980.121RANDOM7.7
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]
0.92-0.950.03
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.261
r_dihedral_angle_4_deg14.688
r_dihedral_angle_3_deg10.979
r_dihedral_angle_1_deg6.293
r_scangle_it3.377
r_scbond_it2.672
r_mcangle_it1.995
r_mcbond_it1.653
r_angle_refined_deg1.652
r_angle_other_deg1.1
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.261
r_dihedral_angle_4_deg14.688
r_dihedral_angle_3_deg10.979
r_dihedral_angle_1_deg6.293
r_scangle_it3.377
r_scbond_it2.672
r_mcangle_it1.995
r_mcbond_it1.653
r_angle_refined_deg1.652
r_angle_other_deg1.1
r_mcbond_other0.644
r_symmetry_vdw_other0.31
r_nbd_refined0.231
r_nbd_other0.22
r_symmetry_hbond_refined0.215
r_xyhbond_nbd_refined0.16
r_chiral_restr0.122
r_symmetry_vdw_refined0.113
r_nbtor_other0.095
r_bond_refined_d0.014
r_gen_planes_refined0.011
r_bond_other_d0.001
r_gen_planes_other
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 Atoms2330
Nucleic Acid Atoms
Solvent Atoms568
Heterogen Atoms23

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling