3GNX

Structure of dehydrated D-xylose isomerase from streptomyces rubiginosus


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1XIGPDB entry 1XIG

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
172786mM Tris-HCl, 33mg/ml crystalline suspension, 0.91M ammonium sulfate, 1mM magnesium sulfate (Hampton Research Ltd.); Soaked in xylitol solution, pH 7.0, temperature 278K
Crystal Properties
Matthews coefficientSolvent content
2.3748.19

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 98.853α = 90
b = 87.65β = 90
c = 94.531γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray293IMAGE PLATESTOEXenocs multilayer optics2007-10-10MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SEALED TUBEOTHER

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
1294.4998.30.1378.14518705187016.836

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 1XIG238.3551870277197.890.162540.160180.2064RANDOM14.967
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]
-0.30.240.06
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.401
r_dihedral_angle_4_deg20.119
r_dihedral_angle_3_deg15.249
r_dihedral_angle_1_deg5.645
r_scangle_it2.736
r_mcangle_it2.11
r_scbond_it1.744
r_angle_refined_deg1.615
r_mcbond_it1.397
r_nbtor_refined0.301
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.401
r_dihedral_angle_4_deg20.119
r_dihedral_angle_3_deg15.249
r_dihedral_angle_1_deg5.645
r_scangle_it2.736
r_mcangle_it2.11
r_scbond_it1.744
r_angle_refined_deg1.615
r_mcbond_it1.397
r_nbtor_refined0.301
r_nbd_refined0.206
r_symmetry_hbond_refined0.169
r_symmetry_vdw_refined0.159
r_xyhbond_nbd_refined0.15
r_metal_ion_refined0.135
r_chiral_restr0.11
r_bond_refined_d0.016
r_gen_planes_refined0.006
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms6062
Nucleic Acid Atoms
Solvent Atoms430
Heterogen Atoms24

Software

Software
Software NamePurpose
STOEdata collection
MOLREPphasing
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling