4JKU

Crystal structure of probable sugar kinase protein from Rhizobium etli CFN 42 complexed with quinaldic acid, NYSGRC Target 14306


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4E3A 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP2980.2M AMMONIUM ACETATE, 0.1M BIS:TRIS: HCL, PH 6.5,25% PEG3350, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.244.16

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 81.529α = 90
b = 91.249β = 90
c = 92.017γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 3152013-02-15SINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSLS BEAMLINE X29A1.075NSLSX29A

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
11.515096.90.06287104812
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)
11.511.5495.10.4646.85080

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 REPLACEMENTTHROUGHOUT4E3A1.5141.08104502523396.670.1680.1660.2053RANDOM21.9008
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]
-0.65-1.352
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.68
r_sphericity_free37.574
r_sphericity_bonded19.526
r_dihedral_angle_4_deg15.848
r_dihedral_angle_3_deg13.383
r_dihedral_angle_1_deg5.779
r_rigid_bond_restr2.707
r_angle_refined_deg1.417
r_chiral_restr0.095
r_bond_refined_d0.009
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.68
r_sphericity_free37.574
r_sphericity_bonded19.526
r_dihedral_angle_4_deg15.848
r_dihedral_angle_3_deg13.383
r_dihedral_angle_1_deg5.779
r_rigid_bond_restr2.707
r_angle_refined_deg1.417
r_chiral_restr0.095
r_bond_refined_d0.009
r_gen_planes_refined0.007
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5008
Nucleic Acid Atoms
Solvent Atoms634
Heterogen Atoms88

Software

Software
Software NamePurpose
SCALEPACKdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
CBASSdata collection
HKL-3000data reduction