5NHB

Crystal structure of xylose isomerase from Piromyces E2 in complex with two Fe2+ ions


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, 0.1 M FeSO4, 0.1 M Hepes pH 7.0
Crystal Properties
Matthews coefficientSolvent content
2.345

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 79.539α = 115.57
b = 79.51β = 89.96
c = 92.23γ = 116.69
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray110IMAGE PLATEMARRESEARCH2014-10-07MSINGLE 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
12.445.385.80.1480.1270.9635.93.5593134.2
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)
12.42.4681.10.490.3860.672.13.3

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_12000040442.445.356358290885.710.246480.244660.28185RANDOM28.773
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]
-1.48-0.560.660.130.460.4
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.512
r_dihedral_angle_3_deg14.701
r_dihedral_angle_4_deg14.693
r_dihedral_angle_1_deg6.189
r_long_range_B_refined2.535
r_long_range_B_other2.476
r_angle_refined_deg1.422
r_angle_other_deg1.061
r_scbond_it0.179
r_chiral_restr0.078
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.512
r_dihedral_angle_3_deg14.701
r_dihedral_angle_4_deg14.693
r_dihedral_angle_1_deg6.189
r_long_range_B_refined2.535
r_long_range_B_other2.476
r_angle_refined_deg1.422
r_angle_other_deg1.061
r_scbond_it0.179
r_chiral_restr0.078
r_mcangle_it0.05
r_mcangle_other0.05
r_mcbond_it0.027
r_mcbond_other0.026
r_scangle_other0.025
r_bond_refined_d0.012
r_scbond_other0.011
r_gen_planes_refined0.006
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 Atoms13866
Nucleic Acid Atoms
Solvent Atoms477
Heterogen Atoms23

Software

Software
Software NamePurpose
REFMACrefinement
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing