3CWH

D-xylose Isomerase in complex with linear product, per-deuterated xylulose


NEUTRON DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4XISPDB entry 4XIS

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1829350MM TRIS-HCL, 38%(NH4)2SO4, 2MM MG2+ XI @ 125 MG/ML, PH=8.0, LIQUID DIFFUSION, T=293K; NATIVE CRYSTAL WERE SOAKED WITH 0.2M PER-DEUTERATED XYLOSE IN D2O BUFFERED IN 50MM TRIS-DCL, PH=7.6 (PD=8.0), 2MM MGCL2
Crystal Properties
Matthews coefficientSolvent content
2.46

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 94.64α = 90
b = 99.97β = 90
c = 103.97γ = 90
Symmetry
Space GroupI 2 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11neutron293AREA DETECTORTIME-OF-FLIGHT MULTIWIRE HE3 NE2004-09-01LLAUE
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1NUCLEAR REACTORPCS

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym 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
12.210089.40.255.85.4218921.5
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.22.3281.30.3823.3

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
NEUTRON DIFFRACTIONMOLECULAR REPLACEMENTFREE RPDB entry 4XIS2.2201707287686.30.2370.288RANDOM20.7
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]
RMS Deviations
KeyRefinement Restraint Deviation
s_angle_d0.962
s_bond_d0.007
s_similar_dist
s_from_restr_planes
s_zero_chiral_vol
s_non_zero_chiral_vol
s_anti_bump_dis_restr
s_rigid_bond_adp_cmpnt
s_similar_adp_cmpnt
s_approx_iso_adps
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3046
Nucleic Acid Atoms
Solvent Atoms227
Heterogen Atoms13

Software

Software
Software NamePurpose
CNSrefinement
SHELXL-97refinement
d*TREKdata reduction
LAUENORMdata scaling
CNSphasing