4LC4

Crystal structure of probable sugar kinase protein from Rhizobium Etli CFN 42 complexed with guanosine


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
2.244.02

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 51.221α = 90
b = 80.879β = 98.4
c = 83.323γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 3152013-04-26SAD
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
11.65097.70.08373.686474
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)
11.61.6378.40.8762.43458

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 4E3A1.742.9473700374799.740.18610.18330.2383RANDOM26.8984
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]
-8.47-10.84-6.4814.95
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.748
r_sphericity_free30.997
r_dihedral_angle_4_deg12.719
r_dihedral_angle_3_deg12.258
r_sphericity_bonded11.383
r_dihedral_angle_1_deg5.277
r_scbond_it3.114
r_mcangle_it2.432
r_rigid_bond_restr2.239
r_mcbond_it1.924
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.748
r_sphericity_free30.997
r_dihedral_angle_4_deg12.719
r_dihedral_angle_3_deg12.258
r_sphericity_bonded11.383
r_dihedral_angle_1_deg5.277
r_scbond_it3.114
r_mcangle_it2.432
r_rigid_bond_restr2.239
r_mcbond_it1.924
r_angle_refined_deg1.396
r_chiral_restr0.15
r_bond_refined_d0.008
r_gen_planes_refined0.005
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5008
Nucleic Acid Atoms
Solvent Atoms689
Heterogen Atoms96

Software

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