5OK1

D10N variant of beta-phosphoglucomutase from Lactococcus lactis trapped with native beta-glucose 1,6-bisphosphate intermediate to 1.9A 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 ca. 12 weeks
Crystal Properties
Matthews coefficientSolvent content
2.2545.37

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 36.71α = 90
b = 74.49β = 90
c = 78.56γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M-F2017-01-30MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I040.97948DiamondI04

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
11.8639.281000.0620.018125.812.918807
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)
11.861.8999.91.9720.5580.5991.213.3

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 REPLACEMENTTHROUGHOUT2WF51.8639.281783492599.930.200110.197810.24559RANDOM42.719
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]
2.6-1.31-1.29
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg41.886
r_dihedral_angle_3_deg13.523
r_dihedral_angle_4_deg10.281
r_dihedral_angle_1_deg6.015
r_long_range_B_refined5.859
r_long_range_B_other5.859
r_scangle_other4.22
r_mcangle_it3.657
r_mcangle_other3.657
r_scbond_it2.72
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg41.886
r_dihedral_angle_3_deg13.523
r_dihedral_angle_4_deg10.281
r_dihedral_angle_1_deg6.015
r_long_range_B_refined5.859
r_long_range_B_other5.859
r_scangle_other4.22
r_mcangle_it3.657
r_mcangle_other3.657
r_scbond_it2.72
r_scbond_other2.717
r_mcbond_it2.527
r_mcbond_other2.525
r_angle_refined_deg1.494
r_angle_other_deg0.948
r_chiral_restr0.076
r_bond_refined_d0.011
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 Atoms67
Heterogen Atoms21

Software

Software
Software NamePurpose
REFMACrefinement
MOLREPphasing
Cootmodel building
XDSdata reduction
xia2data scaling