7NZO

D-lyxose isomerasefrom the hyperthermophilic archaeon Thermofilum sp


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1MICROBATCH7293150 mM Potassium bromide, 30% w/v PEG 2000 MME
Crystal Properties
Matthews coefficientSolvent content
2.3146.8

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 47.77α = 90
b = 86.91β = 112.93
c = 54.03γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER2 XE 16M2021-03-02MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I030.97625DiamondI03

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
11.6739.2692.20.99919.46.243436
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.671.70.326

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE2Y0O1.6739.25243408205392.1320.1810.17920.210741.016
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]
2.5350.653-2.531-0.409
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.862
r_dihedral_angle_4_deg16.665
r_dihedral_angle_3_deg13.972
r_lrange_it8.334
r_scangle_it6.553
r_dihedral_angle_1_deg6.396
r_scbond_it4.8
r_mcangle_it4.241
r_mcbond_it3.34
r_angle_refined_deg1.612
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.862
r_dihedral_angle_4_deg16.665
r_dihedral_angle_3_deg13.972
r_lrange_it8.334
r_scangle_it6.553
r_dihedral_angle_1_deg6.396
r_scbond_it4.8
r_mcangle_it4.241
r_mcbond_it3.34
r_angle_refined_deg1.612
r_nbtor_refined0.318
r_nbd_refined0.208
r_symmetry_nbd_refined0.194
r_symmetry_xyhbond_nbd_refined0.158
r_xyhbond_nbd_refined0.153
r_chiral_restr0.114
r_ncsr_local_group_10.071
r_gen_planes_refined0.01
r_bond_refined_d0.009
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2907
Nucleic Acid Atoms
Solvent Atoms247
Heterogen Atoms46

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
MoRDaphasing