5NHD

Crystal structure of xylose isomerase from Piromyces E2 in complex with 2 Ni2+ 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 DROP729413-15 % PEG3350, 10 mM NiCl2, 0.1 M Hepes pH 7.0
Crystal Properties
Matthews coefficientSolvent content
2.345

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 78.719α = 115.14
b = 79.04β = 90.36
c = 92.01γ = 117.01
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray110IMAGE PLATEMARRESEARCH2014-10-09MSINGLE 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
11.839.491.40.0880.0670.99383.81469165.7
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)
11.81.8387.30.4910.3610.7191.93.8

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_12000040441.839.4139501738291.40.154550.153490.17478RANDOM19.449
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]
-0.16-0.020.010.050.010.04
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.912
r_dihedral_angle_4_deg12.875
r_dihedral_angle_3_deg12.786
r_dihedral_angle_1_deg5.784
r_long_range_B_refined5.399
r_long_range_B_other5.109
r_scangle_other2.287
r_scbond_it1.486
r_scbond_other1.451
r_angle_refined_deg1.37
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.912
r_dihedral_angle_4_deg12.875
r_dihedral_angle_3_deg12.786
r_dihedral_angle_1_deg5.784
r_long_range_B_refined5.399
r_long_range_B_other5.109
r_scangle_other2.287
r_scbond_it1.486
r_scbond_other1.451
r_angle_refined_deg1.37
r_mcangle_other1.306
r_mcangle_it1.305
r_angle_other_deg1.017
r_mcbond_it0.813
r_mcbond_other0.81
r_chiral_restr0.083
r_bond_refined_d0.011
r_gen_planes_refined0.008
r_bond_other_d0.005
r_gen_planes_other0.004
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 Atoms13871
Nucleic Acid Atoms
Solvent Atoms1751
Heterogen Atoms223

Software

Software
Software NamePurpose
REFMACrefinement
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing