5OK0

Structure of the D10N mutant of beta-phosphoglucomutase from Lactococcus lactis trapped with native reaction intermediate beta-glucose 1,6-bisphosphate to 2.2A resolution.


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.229124-34% PEG 4000 200mM Tris pH 7.5 200mM sodium acetate harvested after 1 week
Crystal Properties
Matthews coefficientSolvent content
2.1943.85

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 36.81α = 90
b = 54.94β = 90
c = 103.34γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 6M2016-07-10MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I040.97950DiamondI04

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)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
12.1548.511000.3390.1480.985.36.211990
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.152.191001.6830.7210.3911.26.4

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 REPLACEMENTTHROUGHOUT2WF52.1548.511137657199.880.22350.22010.29234RANDOM31.793
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]
-1.75-0.872.62
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg43.342
r_dihedral_angle_3_deg15.83
r_dihedral_angle_4_deg11.012
r_dihedral_angle_1_deg6.524
r_long_range_B_refined4.902
r_long_range_B_other4.901
r_scangle_other3.546
r_mcangle_other2.782
r_mcangle_it2.781
r_scbond_it2.186
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg43.342
r_dihedral_angle_3_deg15.83
r_dihedral_angle_4_deg11.012
r_dihedral_angle_1_deg6.524
r_long_range_B_refined4.902
r_long_range_B_other4.901
r_scangle_other3.546
r_mcangle_other2.782
r_mcangle_it2.781
r_scbond_it2.186
r_scbond_other2.184
r_mcbond_it1.774
r_mcbond_other1.739
r_angle_refined_deg1.495
r_angle_other_deg0.997
r_chiral_restr0.08
r_bond_refined_d0.012
r_gen_planes_refined0.006
r_bond_other_d0.002
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
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1680
Nucleic Acid Atoms
Solvent Atoms84
Heterogen Atoms26

Software

Software
Software NamePurpose
REFMACrefinement
Cootmodel building
XDSdata reduction
xia2data scaling