4D06

Bacterial chalcone isomerase complexed with naringenin


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4C9SPDB ENTRY 4C9S

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
17.50.1 M HEPES PH 7.5, 0.2 M SODIUM CHLORIDE, 1.6 M AMMONIUM SULFATE, 380 MIKROM NARINGENIN CHALCONE DISSOLVED IN ETHANOL
Crystal Properties
Matthews coefficientSolvent content
4.4772.5

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 181.165α = 90
b = 187.991β = 90
c = 196.221γ = 90
Symmetry
Space GroupI 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6MMIRROR2013-06-06MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONBESSY BEAMLINE 14.1BESSY14.1

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
125099.50.128.943.5436945227.2
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)
122.1298.40.621.93.4

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 4C9S249.182130761121599.80.141360.140230.16277RANDOM24.527
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]
3.34-0.53-2.81
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.493
r_dihedral_angle_4_deg15.796
r_dihedral_angle_3_deg12.025
r_dihedral_angle_1_deg6.736
r_angle_refined_deg1.938
r_mcangle_it1.686
r_scbond_it1.493
r_mcbond_it1.021
r_mcbond_other1.021
r_angle_other_deg0.994
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.493
r_dihedral_angle_4_deg15.796
r_dihedral_angle_3_deg12.025
r_dihedral_angle_1_deg6.736
r_angle_refined_deg1.938
r_mcangle_it1.686
r_scbond_it1.493
r_mcbond_it1.021
r_mcbond_other1.021
r_angle_other_deg0.994
r_chiral_restr0.121
r_bond_refined_d0.019
r_gen_planes_refined0.011
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_mcangle_other
r_scbond_other
r_scangle_it
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms13242
Nucleic Acid Atoms
Solvent Atoms1895
Heterogen Atoms197

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing