5NH9

Crystal structure of xylose isomerase from Piromyces E2 in complex with two Mn2+ 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 MnCl2, 0.1 M Hepes pH 7.0
Crystal Properties
Matthews coefficientSolvent content
2.345

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 78.69α = 115.37
b = 79.4β = 90.04
c = 92.08γ = 117.07
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray110IMAGE PLATEMARRESEARCH2014-09-23MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODEBRUKER AXS MICROSTAR-H1.5148

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
12.0746.792.40.110.0950.9819.33.9981851.8
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)
12.072.159.70.4350.3610.5842.72.9

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_12000040442.0846.793209487793.20.169590.167850.20266RANDOM17.225
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]
-0.11-0.09-0.030.040.020.07
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.079
r_dihedral_angle_3_deg13.643
r_dihedral_angle_4_deg13.316
r_dihedral_angle_1_deg5.759
r_long_range_B_refined4.531
r_long_range_B_other4.258
r_scangle_other1.815
r_angle_refined_deg1.368
r_mcangle_it1.183
r_mcangle_other1.183
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.079
r_dihedral_angle_3_deg13.643
r_dihedral_angle_4_deg13.316
r_dihedral_angle_1_deg5.759
r_long_range_B_refined4.531
r_long_range_B_other4.258
r_scangle_other1.815
r_angle_refined_deg1.368
r_mcangle_it1.183
r_mcangle_other1.183
r_scbond_it1.136
r_scbond_other1.129
r_angle_other_deg1.01
r_mcbond_it0.698
r_mcbond_other0.697
r_chiral_restr0.081
r_bond_refined_d0.012
r_gen_planes_refined0.007
r_bond_other_d0.005
r_gen_planes_other0.005
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 Atoms1522
Heterogen Atoms143

Software

Software
Software NamePurpose
REFMACrefinement
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing