6YDK

Substrate-free P146A variant of beta-phosphoglucomutase from Lactococcus lactis


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.5290PEG 4000 (24% w/v), sodium acetate (200 mM), TRIS (100 mM), HEPES (50 mM), magnesium chloride (5 mM), EDTA (1 mM), sodium azide (2 mM), beta-phosphoglucomutase (0.5 mM). Seeded with 10,000x dilution of much smaller protein crystals grown under the same conditions but with 0.2 mM beta-phosphoglucomutase.
Crystal Properties
Matthews coefficientSolvent content
9.6287.21

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 53.3α = 90
b = 56.24β = 90
c = 77.66γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M-F2018-02-24MSINGLE 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)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
12.0243.9598.80.0750.0810.0310.99914.46.61568332.196
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)
12.022.0588.90.9531.090.5060.5561.23.7

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 REPLACEMENTTHROUGHOUT2WHE2.0243.951486377798.490.21740.21560.2507RANDOM42.707
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]
-0.27-0.360.63
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg41.886
r_dihedral_angle_4_deg22.923
r_dihedral_angle_3_deg15.025
r_dihedral_angle_1_deg6.164
r_angle_refined_deg1.489
r_angle_other_deg0.958
r_chiral_restr0.08
r_bond_refined_d0.011
r_gen_planes_refined0.006
r_bond_other_d0.002
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg41.886
r_dihedral_angle_4_deg22.923
r_dihedral_angle_3_deg15.025
r_dihedral_angle_1_deg6.164
r_angle_refined_deg1.489
r_angle_other_deg0.958
r_chiral_restr0.08
r_bond_refined_d0.011
r_gen_planes_refined0.006
r_bond_other_d0.002
r_gen_planes_other0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1706
Nucleic Acid Atoms
Solvent Atoms34
Heterogen Atoms1

Software

Software
Software NamePurpose
XDSdata reduction
xia2data scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction