1E0X | pdb_00001e0x

XYLANASE 10A FROM SREPTOMYCES LIVIDANS. XYLOBIOSYL-ENZYME INTERMEDIATE AT 1.65 A


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelOtherNATIVE STRUCTURE AT 1.2

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
17.5PROTEIN WAS CRYSTALLISED WITH 18 % PEG 5000 AS PRECIPITANT, 100MM HEPES PH 7.5 AS BUFFER, 10% ISOPROPANOL, CRYSTAL WERE SOAKED IN PRESENCE OF POWDERED SUBSTRATE FOR 12 HOURS. 15% GLYCEROL WAS ADDED AS CRYOPROTECTANT
Crystal Properties
Matthews coefficientSolvent content
2.744

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 49.21α = 90
b = 81.06β = 102.79
c = 72.81γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATEMARRESEARCHLONG MIRRORS (MSC)1997-11-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU RU200

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
11.6515990.03335.63.566881211.8
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)
11.651.71940.09712.94.8

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTNATIVE STRUCTURE AT 1.21.6515634153381990.1260.140.162RANDOM
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]
RMS Deviations
KeyRefinement Restraint Deviation
p_transverse_tor27.8
p_staggered_tor12.3
p_planar_tor4.7
p_scangle_it2.885
p_scbond_it2.301
p_mcangle_it1.994
p_mcbond_it1.448
p_multtor_nbd0.26
p_singtor_nbd0.16
p_xyhbond_nbd0.14
RMS Deviations
KeyRefinement Restraint Deviation
p_transverse_tor27.8
p_staggered_tor12.3
p_planar_tor4.7
p_scangle_it2.885
p_scbond_it2.301
p_mcangle_it1.994
p_mcbond_it1.448
p_multtor_nbd0.26
p_singtor_nbd0.16
p_xyhbond_nbd0.14
p_chiral_restr0.121
p_planar_d0.034
p_angle_d0.028
p_plane_restr0.026
p_bond_d0.012
p_angle_deg
p_hb_or_metal_coord
p_xhyhbond_nbd
p_orthonormal_tor
p_special_tor
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4760
Nucleic Acid Atoms
Solvent Atoms717
Heterogen Atoms54

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing