4GME

Crystal structure of mannonate dehydratase (target EFI-502209) from caulobacter crescentus cb15 complexed with magnesium and d-mannonate


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3VCN 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
18.50.1M AMMONIUM SULFATE, 0.1M TRIS-HCL, PH 8.5, 25% PEG3350, 10% GLYCEROL, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 294K
Crystal Properties
Matthews coefficientSolvent content
2.1241.94

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 115.801α = 90
b = 115.801β = 90
c = 118.131γ = 90
Symmetry
Space GroupI 4

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315MIRRORS2011-11-17MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSLS BEAMLINE X29ANSLSX29A

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym 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
1250910.082124.153061-524.361
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)
122.031000.452.74.2

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 REPLACEMENTTHROUGHOUT3VCN236.6246026141090.30.156940.15570.19553RANDOM30.59
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]
-5.39-5.3910.78
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.044
r_dihedral_angle_4_deg16.839
r_dihedral_angle_3_deg13.341
r_dihedral_angle_1_deg5.953
r_angle_refined_deg1.223
r_chiral_restr0.082
r_bond_refined_d0.008
r_gen_planes_refined0.006
r_bond_other_d
r_angle_other_deg
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.044
r_dihedral_angle_4_deg16.839
r_dihedral_angle_3_deg13.341
r_dihedral_angle_1_deg5.953
r_angle_refined_deg1.223
r_chiral_restr0.082
r_bond_refined_d0.008
r_gen_planes_refined0.006
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_it
r_mcbond_other
r_mcangle_it
r_scbond_it
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms6312
Nucleic Acid Atoms
Solvent Atoms507
Heterogen Atoms27

Software

Software
Software NamePurpose
PHASERphasing
REFMACrefinement
HKL-3000data reduction
HKL-3000data scaling