2OX4

Crystal structure of putative dehydratase from Zymomonas mobilis ZM4


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP8.5294100mM Tris-HCl, pH 8.5, 30% PEG 4000, 200mM Lithium sulfate, 10% Glycerol, VAPOR DIFFUSION, SITTING DROP, temperature 294K
Crystal Properties
Matthews coefficientSolvent content
2.1743.46

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 190.178α = 90
b = 190.409β = 90
c = 85.922γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMAR CCD 165 mmMIRRORS2006-02-09MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 31-ID0.97960APS31-ID

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (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
11.8501000.0940.0754.86.7288410288410-516.777
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.81.8699.80.480.432.26.228540

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB entry 2GL51.820278981278981875899.640.145130.145130.143860.18553RANDOM18.369
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]
-0.180.23-0.05
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.12
r_dihedral_angle_4_deg18.864
r_dihedral_angle_3_deg15.781
r_scangle_it8.56
r_dihedral_angle_1_deg7.896
r_scbond_it6.099
r_mcangle_it4.108
r_mcbond_it3.18
r_angle_refined_deg1.171
r_nbtor_refined0.309
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.12
r_dihedral_angle_4_deg18.864
r_dihedral_angle_3_deg15.781
r_scangle_it8.56
r_dihedral_angle_1_deg7.896
r_scbond_it6.099
r_mcangle_it4.108
r_mcbond_it3.18
r_angle_refined_deg1.171
r_nbtor_refined0.309
r_nbd_refined0.181
r_xyhbond_nbd_refined0.174
r_symmetry_hbond_refined0.169
r_chiral_restr0.157
r_symmetry_vdw_refined0.155
r_bond_refined_d0.01
r_gen_planes_refined0.005
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms24692
Nucleic Acid Atoms
Solvent Atoms3160
Heterogen Atoms96

Software

Software
Software NamePurpose
MOLREPphasing
REFMACrefinement
MAR345data collection
HKL-2000data reduction
HKL-2000data scaling