7P5O

Crystal structure of Aspergillus fumigatus phosphoglucomutase in complex with the reaction intermediate


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP291.1590 mM sodium fluoride, 90 mM sodium bromide, 90 mM sodium iodide, 100 mM Tris-bicine pH 8.5, 20% v/v polyethylene glycol 550 MME, 10 % w/v polyethylene glycol 20000
Crystal Properties
Matthews coefficientSolvent content
2.5952.54

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 98.57α = 90
b = 209.61β = 90
c = 61.2γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 4M2016-10-02MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE MASSIF-30.967700ESRFMASSIF-3

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
12.4889.298.40.99411.24.244960
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)
12.482.530.795

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 REPLACEMENTTHROUGHOUT5EPC2.4889.242710225098.390.20410.20110.2584RANDOM37.597
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]
-2.750.242.51
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.691
r_dihedral_angle_4_deg24.033
r_dihedral_angle_3_deg18.859
r_dihedral_angle_1_deg7.523
r_angle_refined_deg1.629
r_angle_other_deg1.272
r_chiral_restr0.094
r_bond_refined_d0.009
r_gen_planes_refined0.006
r_bond_other_d0.001
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.691
r_dihedral_angle_4_deg24.033
r_dihedral_angle_3_deg18.859
r_dihedral_angle_1_deg7.523
r_angle_refined_deg1.629
r_angle_other_deg1.272
r_chiral_restr0.094
r_bond_refined_d0.009
r_gen_planes_refined0.006
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms8545
Nucleic Acid Atoms
Solvent Atoms510
Heterogen Atoms42

Software

Software
Software NamePurpose
MOLREPphasing
REFMACrefinement
PDB_EXTRACTdata extraction
autoPROCdata reduction
autoPROCdata scaling