6HDK

R49A variant of beta-phosphoglucomutase from Lactococcus lactis complexed with aluminium tetrafluoride and beta-G6P to 1.2 A.


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2WF6 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.229124-34% PEG 4000 200mM sodium acetate 50mM TRIS pH 7.5
Crystal Properties
Matthews coefficientSolvent content
2.1843.6

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 37.23α = 90
b = 54.29β = 90
c = 104.24γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 6M2016-04-27MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I030.97625DiamondI03

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
11.2454.291000.0990.1070.040.99910.1760728
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)
11.241.2697.91.0191.1310.480.535.3

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 REPLACEMENTTHROUGHOUT2WF61.2452.1757667298399.830.137460.135930.16724RANDOM16.05
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]
-0.31-0.711.02
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.315
r_dihedral_angle_4_deg24.067
r_sphericity_free23.33
r_dihedral_angle_3_deg11.788
r_sphericity_bonded10.782
r_dihedral_angle_1_deg5.52
r_long_range_B_other3.508
r_long_range_B_refined3.507
r_scangle_other2.899
r_scbond_it2.401
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.315
r_dihedral_angle_4_deg24.067
r_sphericity_free23.33
r_dihedral_angle_3_deg11.788
r_sphericity_bonded10.782
r_dihedral_angle_1_deg5.52
r_long_range_B_other3.508
r_long_range_B_refined3.507
r_scangle_other2.899
r_scbond_it2.401
r_scbond_other2.4
r_mcangle_other2.155
r_mcangle_it2.142
r_rigid_bond_restr1.785
r_mcbond_it1.626
r_mcbond_other1.609
r_angle_refined_deg1.496
r_angle_other_deg1.067
r_chiral_restr0.078
r_bond_refined_d0.01
r_gen_planes_refined0.009
r_bond_other_d0.001
r_gen_planes_other0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1683
Nucleic Acid Atoms
Solvent Atoms209
Heterogen Atoms36

Software

Software
Software NamePurpose
REFMACrefinement
xia2data reduction
xia2data scaling
MOLREPphasing