7CJ4

Crystal structure of homo dimeric D-allulose 3-epimerase from Methylomonas sp.


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP8.5293magnesium chloride, Tris, PEG3350
Crystal Properties
Matthews coefficientSolvent content
1.9938.24

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 45.73α = 90
b = 80.72β = 90
c = 139.45γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 S 6M2018-12-09MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPHOTON FACTORY BEAMLINE BL-5A1.0Photon FactoryBL-5A

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim 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
12.0843.4599.80.1040.1130.99813.476.4193185131.72
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.082.131000.5350.580.8783.566.653

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 REPLACEMENTTHROUGHOUT5ZFS2.0843.4530186160599.830.18930.1850.2689RANDOM26.083
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]
-0.450.79-0.34
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.771
r_dihedral_angle_4_deg18.082
r_dihedral_angle_3_deg16.305
r_dihedral_angle_1_deg6.405
r_rigid_bond_restr3.986
r_angle_other_deg1.209
r_angle_refined_deg1.199
r_chiral_restr0.045
r_bond_refined_d0.004
r_gen_planes_refined0.003
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.771
r_dihedral_angle_4_deg18.082
r_dihedral_angle_3_deg16.305
r_dihedral_angle_1_deg6.405
r_rigid_bond_restr3.986
r_angle_other_deg1.209
r_angle_refined_deg1.199
r_chiral_restr0.045
r_bond_refined_d0.004
r_gen_planes_refined0.003
r_bond_other_d
r_gen_planes_other
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4398
Nucleic Acid Atoms
Solvent Atoms351
Heterogen Atoms2

Software

Software
Software NamePurpose
XDSdata reduction
XSCALEdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
MOLREPphasing