6IQV

Crystal Structure of Cell Surface Glyceraldehyde-3-Phosphate Dehydrogenase Complexed with Hg2+ from Lactobacillus plantarum


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5J9G 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP529325% (w/v) PEG 1500, 0.1M MIB buffer (pH 5.0)
Crystal Properties
Matthews coefficientSolvent content
2.8456.64

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 126.043α = 90
b = 172.949β = 90
c = 149.235γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 2M-F2018-05-31MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPHOTON FACTORY BEAMLINE AR-NE3A1.0085Photon FactoryAR-NE3A

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)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
12.13101.8699.90.0916.69.19088337.34
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.132.1799.30.5216.8

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 REPLACEMENTTHROUGHOUT5J9G2.13101.8686296455099.260.204640.201970.229RANDOM42.213
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]
-0.040.08-0.04
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg43.559
r_dihedral_angle_3_deg16.897
r_dihedral_angle_4_deg16.414
r_long_range_B_refined9.27
r_dihedral_angle_1_deg7.706
r_mcangle_it5.09
r_scbond_it4.837
r_mcbond_it3.684
r_angle_refined_deg1.97
r_chiral_restr0.131
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg43.559
r_dihedral_angle_3_deg16.897
r_dihedral_angle_4_deg16.414
r_long_range_B_refined9.27
r_dihedral_angle_1_deg7.706
r_mcangle_it5.09
r_scbond_it4.837
r_mcbond_it3.684
r_angle_refined_deg1.97
r_chiral_restr0.131
r_bond_refined_d0.018
r_gen_planes_refined0.009
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
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_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_it
r_scangle_other
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms10078
Nucleic Acid Atoms
Solvent Atoms604
Heterogen Atoms43

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing