5NH4

Crystal structure of xylose isomerase from Piromyces E2 in complex with one Mg2+ ions and glycerol


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5NH5 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP729413-16 % PEG 3350, 0.01 M MgCl2, 0,1 M Hepes pH 7
Crystal Properties
Matthews coefficientSolvent content
2.345

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 78.606α = 115.5
b = 79.365β = 90.15
c = 92.096γ = 116.92
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray110IMAGE PLATEMARRESEARCH2014-09-04MSINGLE 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
11.846.693.40.0890.0640.9958.441499116.5
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)
11.81.8380.70.350.260.6882.63.6

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 REPLACEMENTTHROUGHOUT5NH51.846.46142387749593.350.195880.194120.22944RANDOM18.034
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]
-0.09-0.05-0.020.030.010.05
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.642
r_dihedral_angle_4_deg14.185
r_dihedral_angle_3_deg13.695
r_dihedral_angle_1_deg6.067
r_long_range_B_refined4.584
r_long_range_B_other4.584
r_scangle_other1.754
r_angle_refined_deg1.482
r_mcangle_other1.135
r_mcangle_it1.134
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.642
r_dihedral_angle_4_deg14.185
r_dihedral_angle_3_deg13.695
r_dihedral_angle_1_deg6.067
r_long_range_B_refined4.584
r_long_range_B_other4.584
r_scangle_other1.754
r_angle_refined_deg1.482
r_mcangle_other1.135
r_mcangle_it1.134
r_scbond_it1.128
r_scbond_other1.128
r_angle_other_deg1.123
r_mcbond_it0.708
r_mcbond_other0.707
r_chiral_restr0.094
r_bond_refined_d0.014
r_gen_planes_refined0.009
r_bond_other_d0.007
r_gen_planes_other0.006
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 Atoms1638
Heterogen Atoms85

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata scaling
Aimlessdata scaling
PHASERphasing
XDSdata reduction