3NA5

Crystal structure of a bacterial phosphoglucomutase, an enzyme important in the virulence of several human pathogens.


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2FUVPDB Entry 2FUV

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.52770.1 M Bis-Tris, 0.3 M magnesium chloride, 20% PEG 3350,0.1% n-octyl-beta D-gluco-pyranoside , pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
2.2445.14

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 81.466α = 90
b = 105.792β = 90
c = 126.797γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray103CCDNOIR-1beamline optics2010-02-21MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALS BEAMLINE 4.2.21.0ALS4.2.2

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
11.742.2799.90.05610.84.7120749
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)
1.71.799.30.4872.33.66

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONREFINEMENTTHROUGHOUTPDB Entry 2FUV1.742.27114594114594606699.870.183550.181760.2178RANDOM18.729
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]
0.34-0.27-0.07
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.737
r_dihedral_angle_4_deg21.832
r_dihedral_angle_3_deg11.866
r_dihedral_angle_1_deg5.69
r_scangle_it3.264
r_scbond_it2.055
r_angle_refined_deg1.456
r_mcangle_it1.151
r_mcbond_it0.688
r_chiral_restr0.124
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.737
r_dihedral_angle_4_deg21.832
r_dihedral_angle_3_deg11.866
r_dihedral_angle_1_deg5.69
r_scangle_it3.264
r_scbond_it2.055
r_angle_refined_deg1.456
r_mcangle_it1.151
r_mcbond_it0.688
r_chiral_restr0.124
r_bond_refined_d0.013
r_gen_planes_refined0.008
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_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms8045
Nucleic Acid Atoms
Solvent Atoms1020
Heterogen Atoms30

Software

Software
Software NamePurpose
d*TREKdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACTdata extraction
d*TREKdata reduction