5NHA

Crystal structure of xylose isomerase from Piromyces sp. E2 in complex with two Mn2+ ions and sorbitol


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 MnCl2, 0.1 M Hepes pH 7.0
Crystal Properties
Matthews coefficientSolvent content
2.345

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 78.961α = 115.67
b = 79.407β = 89.44
c = 91.284γ = 116.92
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray110IMAGE PLATEMARRESEARCH2015-03-09MSINGLE 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
11.846.993.60.0940.0680.99511.63.9151276
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)
11.81.8379.60.4820.3780.5832.13.2

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_12000040441.846.9143710755793.580.156740.155440.18141RANDOM15.707
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]
-0.1-0.030.060.030.03
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.82
r_dihedral_angle_4_deg13.151
r_dihedral_angle_3_deg12.917
r_dihedral_angle_1_deg5.743
r_long_range_B_refined4.031
r_long_range_B_other3.757
r_angle_refined_deg1.477
r_scangle_other1.279
r_angle_other_deg0.954
r_mcangle_it0.925
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.82
r_dihedral_angle_4_deg13.151
r_dihedral_angle_3_deg12.917
r_dihedral_angle_1_deg5.743
r_long_range_B_refined4.031
r_long_range_B_other3.757
r_angle_refined_deg1.477
r_scangle_other1.279
r_angle_other_deg0.954
r_mcangle_it0.925
r_mcangle_other0.925
r_scbond_it0.81
r_scbond_other0.783
r_mcbond_it0.527
r_mcbond_other0.526
r_chiral_restr0.095
r_bond_refined_d0.012
r_gen_planes_refined0.007
r_bond_other_d0.002
r_gen_planes_other0.001
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 Atoms1984
Heterogen Atoms76

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing