4K8P

Crystal structure of probable sugar kinase protein from Rhizobium etli CFN 42 complexed with 2-ethylbenzyl alcohol


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4E3APDB ENTRY 4E3A

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.52980.2M AMMONIUM ACETATE, 0.1M BIS:TRIS:HCL, PH 6.5,25% PEG3350, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.1943.79

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 51.429α = 90
b = 80.818β = 97.85
c = 82.591γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 3152013-03-28SAD
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
11.495084.10.0648.62.991641
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)
11.491.5226.80.7831.51468

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 4E3A1.540.0991116454785.240.18750.18490.2365RANDOM25.8937
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]
-2.13-1.490.941.19
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.227
r_sphericity_free35.909
r_dihedral_angle_4_deg15.724
r_sphericity_bonded14.937
r_dihedral_angle_3_deg13.742
r_dihedral_angle_1_deg5.551
r_rigid_bond_restr2.326
r_angle_refined_deg1.248
r_chiral_restr0.086
r_bond_refined_d0.008
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.227
r_sphericity_free35.909
r_dihedral_angle_4_deg15.724
r_sphericity_bonded14.937
r_dihedral_angle_3_deg13.742
r_dihedral_angle_1_deg5.551
r_rigid_bond_restr2.326
r_angle_refined_deg1.248
r_chiral_restr0.086
r_bond_refined_d0.008
r_gen_planes_refined0.005
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5038
Nucleic Acid Atoms
Solvent Atoms528
Heterogen Atoms68

Software

Software
Software NamePurpose
SCALEPACKdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
CBASSdata collection
HKL-2000data reduction