4O5S

Crystal structure of Diels-Alderase CE11


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.5293protein solution (11.7 mg/mL, in 25 mM HEPES, pH 7.5, 150 mM NaCl) was mixed with reservoir solution containing 24.0% w/v PEG 3350 and 0.2 M ammonium nitrate, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
1.8633.81

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 43.04α = 84.12
b = 46.15β = 83.01
c = 76.91γ = 66.18
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELPSI PILATUS 6M2012-09-02MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X06DA1.00SLSX06DA

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
11.842.2960.0488143.547771-3
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)
11.81.992.30.2373.943.486849

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 REPLACEMENTTHROUGHOUT1E1A1.842.1545382238996.030.18720.184850.23266RANDOM29.032
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]
-1.53-0.73-0.321.351.13-0.64
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.787
r_dihedral_angle_4_deg20.895
r_dihedral_angle_3_deg14.137
r_dihedral_angle_1_deg7.311
r_long_range_B_refined5.301
r_long_range_B_other5.284
r_scangle_other3.85
r_mcangle_it3.315
r_mcangle_other3.315
r_scbond_it2.645
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.787
r_dihedral_angle_4_deg20.895
r_dihedral_angle_3_deg14.137
r_dihedral_angle_1_deg7.311
r_long_range_B_refined5.301
r_long_range_B_other5.284
r_scangle_other3.85
r_mcangle_it3.315
r_mcangle_other3.315
r_scbond_it2.645
r_scbond_other2.644
r_mcbond_it2.383
r_mcbond_other2.382
r_angle_refined_deg1.71
r_angle_other_deg0.832
r_chiral_restr0.103
r_bond_refined_d0.014
r_gen_planes_refined0.009
r_bond_other_d0.001
r_gen_planes_other0.001
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_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4713
Nucleic Acid Atoms
Solvent Atoms135
Heterogen Atoms

Software

Software
Software NamePurpose
PHASERphasing
REFMACrefinement
XDSdata reduction
SADABSdata scaling