3KL5

Structure Analysis of a Xylanase From Glycosyl Hydrolase Family Thirty: Carbohydrate Ligand Complexes Reveal this Family of Enzymes Unique Mechanism of Substrate Specificity and Recognition


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3KL0PDB ENTRY 3KL0

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP294.6200 mM sodium tartrate, 200 mM sodium malonate, pH 7.0, 19% PEG3350 Crystal was soaked in mother liquor with cryoprotectent and aldotetrauronic acid, VAPOR DIFFUSION, SITTING DROP, temperature 294.6K
Crystal Properties
Matthews coefficientSolvent content
2.4249.07

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 137.723α = 90
b = 194.008β = 90
c = 65.707γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray105CCDRAYONIX MX-3252009-02-01MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRL BEAMLINE BL12-20.97946SSRLBL12-2

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
12.595097.90.08610.66.654718
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)
2.592.6885.40.8923.24686

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 3KL02.595054602277897.550.2430.2410.29RANDOM73.226
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]
-0.552.66-2.11
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg42.126
r_dihedral_angle_4_deg20.197
r_dihedral_angle_3_deg16.742
r_dihedral_angle_1_deg6
r_scangle_it2.084
r_angle_refined_deg1.246
r_scbond_it1.208
r_mcangle_it1.004
r_mcbond_it0.526
r_chiral_restr0.08
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg42.126
r_dihedral_angle_4_deg20.197
r_dihedral_angle_3_deg16.742
r_dihedral_angle_1_deg6
r_scangle_it2.084
r_angle_refined_deg1.246
r_scbond_it1.208
r_mcangle_it1.004
r_mcbond_it0.526
r_chiral_restr0.08
r_bond_refined_d0.011
r_gen_planes_refined0.005
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms12259
Nucleic Acid Atoms
Solvent Atoms47
Heterogen Atoms127

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
Blu-Icedata collection
Web-Icedata collection