6YDJ

P146A variant of beta-phosphoglucomutase from Lactococcus lactis in complex with glucose 6-phosphate and trifluoromagnesate


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2WF5 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.5290PEG 4000 (32% w/v), sodium acetate (200 mM), TRIS (100 mM), HEPES (13 mM), magnesium chloride (5 mM), EDTA (200 uM), sodium azide (500 uM), sodium fluoride (15 mM), glucose 6-phosphate (10 mM), beta-phosphoglucomutase (0.4 mM)
Crystal Properties
Matthews coefficientSolvent content
2.1743.3

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 37.08α = 90
b = 54.25β = 90
c = 104.32γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M-F2018-02-10MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I04-10.91587DiamondI04-1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)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
11.0454.2599.90.0670.0730.0280.99912.46.71017307.445
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.041.0699.31.1381.2950.6090.5441.14.4

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 REPLACEMENTTHROUGHOUT2WF51.0452.2196597504199.810.15060.14970.1685RANDOM12.63
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]
-0.01-0.360.37
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.791
r_dihedral_angle_4_deg24.108
r_sphericity_free22.635
r_dihedral_angle_3_deg11.449
r_sphericity_bonded6.597
r_dihedral_angle_1_deg5.25
r_rigid_bond_restr2.057
r_angle_refined_deg1.473
r_angle_other_deg0.908
r_chiral_restr0.074
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.791
r_dihedral_angle_4_deg24.108
r_sphericity_free22.635
r_dihedral_angle_3_deg11.449
r_sphericity_bonded6.597
r_dihedral_angle_1_deg5.25
r_rigid_bond_restr2.057
r_angle_refined_deg1.473
r_angle_other_deg0.908
r_chiral_restr0.074
r_bond_refined_d0.009
r_gen_planes_refined0.009
r_bond_other_d0.003
r_gen_planes_other0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1678
Nucleic Acid Atoms
Solvent Atoms209
Heterogen Atoms31

Software

Software
Software NamePurpose
XDSdata reduction
xia2data scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction