6HDJ

R49K variant of beta-phosphoglucomutase from Lactococcus lactis complexed 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
2.1743.36

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 104.21α = 90
b = 37.22β = 90
c = 54.22γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2016-04-28MSINGLE 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
11.1648.195.40.0840.090.0330.99911.27.370516
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)
11.161.1888.51.0821.180.460.5546.2

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 REPLACEMENTTHROUGHOUT2WF61.1648.166963349395.350.144260.143140.16567RANDOM16.045
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]
0.32-0.520.2
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.543
r_sphericity_free21.317
r_dihedral_angle_4_deg20.133
r_sphericity_bonded12.501
r_dihedral_angle_3_deg10.836
r_dihedral_angle_1_deg5.615
r_long_range_B_other3.159
r_long_range_B_refined3.158
r_scangle_other2.617
r_scbond_it2.18
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.543
r_sphericity_free21.317
r_dihedral_angle_4_deg20.133
r_sphericity_bonded12.501
r_dihedral_angle_3_deg10.836
r_dihedral_angle_1_deg5.615
r_long_range_B_other3.159
r_long_range_B_refined3.158
r_scangle_other2.617
r_scbond_it2.18
r_scbond_other2.18
r_mcangle_other2.153
r_mcangle_it2.142
r_rigid_bond_restr1.808
r_mcbond_it1.606
r_mcbond_other1.566
r_angle_refined_deg1.502
r_angle_other_deg1.087
r_chiral_restr0.079
r_bond_refined_d0.01
r_gen_planes_refined0.009
r_gen_planes_other0.002
r_bond_other_d0.001
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 Atoms1687
Nucleic Acid Atoms
Solvent Atoms177
Heterogen Atoms34

Software

Software
Software NamePurpose
REFMACrefinement
xia2data reduction
xia2data scaling
MOLREPphasing