5NH8

Crystal structure of xylose isomerase from Piromyces E2 in complex with two Ca2+ ions and xylose


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5NH5D_1200004044

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP29413-15 % PEG3350, 10 mM CaCl2, 0.1 M Hepes pH 7.0
Crystal Properties
Matthews coefficientSolvent content
2.345

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 78.764α = 115.41
b = 79.337β = 89.91
c = 91.926γ = 117.16
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray110IMAGE PLATEMARRESEARCH2015-02-25MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODEBRUKER AXS MICROSTAR-H1.5418

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rpim I (All)CC (Half)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
11.8646.792.60.090.0710.99510.641363869.3
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.861.8975.70.4880.3840.6022.13.2

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 REPLACEMENTTHROUGHOUTD_12000040441.8646.7129514682993.670.177120.175850.20136RANDOM20.21
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]
-0.19-0.110.070.030.070.06
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.041
r_dihedral_angle_3_deg13.042
r_dihedral_angle_4_deg12.574
r_dihedral_angle_1_deg5.684
r_long_range_B_refined4.9
r_long_range_B_other4.554
r_scangle_other1.522
r_angle_refined_deg1.238
r_mcangle_it1.162
r_mcangle_other1.162
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.041
r_dihedral_angle_3_deg13.042
r_dihedral_angle_4_deg12.574
r_dihedral_angle_1_deg5.684
r_long_range_B_refined4.9
r_long_range_B_other4.554
r_scangle_other1.522
r_angle_refined_deg1.238
r_mcangle_it1.162
r_mcangle_other1.162
r_scbond_it0.984
r_scbond_other0.948
r_angle_other_deg0.929
r_mcbond_it0.69
r_mcbond_other0.69
r_chiral_restr0.072
r_bond_refined_d0.009
r_gen_planes_refined0.006
r_bond_other_d0.004
r_gen_planes_other0.003
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms13876
Nucleic Acid Atoms
Solvent Atoms1620
Heterogen Atoms160

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing