2E22

Crystal structure of xanthan lyase in complex with mannose


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1J0MPDB ENTRY 1J0M

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP929322% PEG 4000, 0.2M ammonium formate, 0.1M sodium Bicine, pH 9, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.4649.93

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 54.358α = 90
b = 91.462β = 90
c = 159.653γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100AREA DETECTORSIEMENS HI-STAR2005-12-20MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODEMACSCIENCE1.5418

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
12.365088.60.0642973824.1
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)
12.362.4542.90.254

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 1J0M2.430.1528495139889.20.1650.1650.21RANDOM25.3
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]
-2.2-3.515.71
RMS Deviations
KeyRefinement Restraint Deviation
c_dihedral_angle_d23.8
c_scangle_it2.67
c_scbond_it1.87
c_mcangle_it1.75
c_angle_deg1.2
c_mcbond_it1.09
c_improper_angle_d0.73
c_bond_d0.005
c_bond_d_na
c_bond_d_prot
RMS Deviations
KeyRefinement Restraint Deviation
c_dihedral_angle_d23.8
c_scangle_it2.67
c_scbond_it1.87
c_mcangle_it1.75
c_angle_deg1.2
c_mcbond_it1.09
c_improper_angle_d0.73
c_bond_d0.005
c_bond_d_na
c_bond_d_prot
c_angle_d
c_angle_d_na
c_angle_d_prot
c_angle_deg_na
c_angle_deg_prot
c_dihedral_angle_d_na
c_dihedral_angle_d_prot
c_improper_angle_d_na
c_improper_angle_d_prot
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5697
Nucleic Acid Atoms
Solvent Atoms230
Heterogen Atoms12

Software

Software
Software NamePurpose
CNSrefinement
FRAMBOdata collection
SAINTdata reduction
SAINTdata scaling
CNSphasing