3HN6

Crystal structure of glucosamine-6-phosphate deaminase from Borrelia burgdorferi


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1NE7PDB entry 1NE7

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP8.3289JCSG+ sparse matrix screen condition B12, 20% PEG 3350, 0.2 M Potassium phosphate pH 8.3, 27.2 mg/mL protein, 0.1 mg/mL Chymotrypsin, crystal tracking ID 203097b12, VAPOR DIFFUSION, SITTING DROP, temperature 289K
Crystal Properties
Matthews coefficientSolvent content
2.2745.82

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 89.9α = 90
b = 82.79β = 109.58
c = 126.99γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRIGAKU SATURN 944+2009-05-19MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU FR-E+ SUPERBRIGHT1.5418

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
12.25096.10.05420.7585968-331.993
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)
12.22.26850.2455.6

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 REPLACEMENTTHROUGHOUTPDB entry 1NE72.25085951433096.220.1880.1850.237RANDOM25.007
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]
-0.16-0.190.45-0.42
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.4
r_dihedral_angle_3_deg15.448
r_dihedral_angle_4_deg11.849
r_dihedral_angle_1_deg5.845
r_scangle_it3.679
r_scbond_it2.24
r_mcangle_it1.413
r_angle_refined_deg1.378
r_mcbond_it0.754
r_chiral_restr0.095
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.4
r_dihedral_angle_3_deg15.448
r_dihedral_angle_4_deg11.849
r_dihedral_angle_1_deg5.845
r_scangle_it3.679
r_scbond_it2.24
r_mcangle_it1.413
r_angle_refined_deg1.378
r_mcbond_it0.754
r_chiral_restr0.095
r_bond_refined_d0.014
r_gen_planes_refined0.006
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms12538
Nucleic Acid Atoms
Solvent Atoms855
Heterogen Atoms27

Software

Software
Software NamePurpose
XSCALEdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction