5NH5

Crystal structure of native xylose isomerase from Piromyces E2


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1A0C1A0C, 1A0D, 1A0E
experimental modelPDB 1A0D1A0C, 1A0D, 1A0E
experimental modelPDB 1A0E1A0C, 1A0D, 1A0E

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP729413-16 % PEG3350, HEPES pH 7
Crystal Properties
Matthews coefficientSolvent content
2.345

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 78.72α = 115.33
b = 79.36β = 90.31
c = 92.21γ = 117
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray110IMAGE PLATEMARRESEARCH2014-06-03MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODEBRUKER AXS MICROSTAR-H1.54

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)R Sym I (Observed)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
11.7941.292.30.0450.0340.99820.63.91506736.5
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)
11.791.8266.70.230.230.9054.93.2

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-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT1A0C, 1A0D, 1A0E1.841.2143101755093.010.124060.122810.140.147820.16RANDOM14.927
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]
-0.02-0.020.01-0.010.02
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.167
r_dihedral_angle_4_deg14.914
r_dihedral_angle_3_deg12.308
r_dihedral_angle_1_deg5.85
r_long_range_B_refined5.527
r_long_range_B_other4.997
r_scangle_other2.348
r_scbond_it1.503
r_scbond_other1.502
r_angle_refined_deg1.488
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms13876
Nucleic Acid Atoms
Solvent Atoms2373
Heterogen Atoms147

Software

Software
Software NamePurpose
REFMACrefinement
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing