1V0K | pdb_00001v0k

Xylanase Xyn10A from Streptomyces lividans in complex with xylobio-deoxynojirimycin 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, PH 5.8, 18% PEG 5K MME, 7.5% ISOPROPANOL
Crystal Properties
Matthews coefficientSolvent content
1.935.3

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 67.08α = 90
b = 46.204β = 90
c = 86.071γ = 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 MULTILAYER2003-10-15MSINGLE 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
11.033097.10.04723.84.2128937
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)
11.031.0593.70.4152.313.5

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-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 1OD81.0327.15122389642196.90.1150.1140.130.1370.16RANDOM7.54
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]
0.82-0.44-0.38
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.343
r_dihedral_angle_4_deg14.392
r_dihedral_angle_3_deg11.22
r_dihedral_angle_1_deg6.555
r_scangle_it2.873
r_scbond_it2.282
r_mcangle_it1.683
r_angle_refined_deg1.572
r_mcbond_it1.404
r_angle_other_deg0.822
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.343
r_dihedral_angle_4_deg14.392
r_dihedral_angle_3_deg11.22
r_dihedral_angle_1_deg6.555
r_scangle_it2.873
r_scbond_it2.282
r_mcangle_it1.683
r_angle_refined_deg1.572
r_mcbond_it1.404
r_angle_other_deg0.822
r_mcbond_other0.546
r_nbd_refined0.317
r_symmetry_vdw_other0.281
r_nbd_other0.236
r_symmetry_hbond_refined0.198
r_xyhbond_nbd_refined0.177
r_nbtor_other0.113
r_chiral_restr0.109
r_symmetry_vdw_refined0.088
r_bond_refined_d0.012
r_gen_planes_refined0.01
r_gen_planes_other0.004
r_bond_other_d0.001
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 Atoms2328
Nucleic Acid Atoms
Solvent Atoms703
Heterogen Atoms18

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling