6ZE4

FAD-dependent oxidoreductase from Chaetomium thermophilum in complex with fragment 4-oxo-N-[(1S)-1-(pyridin-3-yl)ethyl]-4-(thiophen-2-yl)butanamide


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 6ZE2 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP5.5293.1517 % (w/v) PEG MME 5000, 0.1 M sodium acetate, pH 5.5, 0.16 M magnesium formate, protein concentration 8 mg/ml
Crystal Properties
Matthews coefficientSolvent content
2.3648

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 93.562α = 90
b = 109.875β = 90
c = 116.113γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2018-05-17MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONBESSY BEAMLINE 14.10.9184BESSY14.1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)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
11.649.3893.50.0880.0970.0390.9988.75.5147085-3.716.8
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.61.6398.51.0091.1080.4410.6591.65.7

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)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 REPLACEMENTTHROUGHOUT6ZE21.649.38146842729993.0910.1720.17220.16970.2022random selection19.643
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]
1.458-0.984-0.474
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.092
r_dihedral_angle_4_deg18.158
r_dihedral_angle_3_deg11.87
r_dihedral_angle_1_deg7.223
r_lrange_it4.372
r_lrange_other4.001
r_scangle_it2.901
r_scangle_other2.901
r_scbond_it1.978
r_scbond_other1.976
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.092
r_dihedral_angle_4_deg18.158
r_dihedral_angle_3_deg11.87
r_dihedral_angle_1_deg7.223
r_lrange_it4.372
r_lrange_other4.001
r_scangle_it2.901
r_scangle_other2.901
r_scbond_it1.978
r_scbond_other1.976
r_mcangle_other1.785
r_mcangle_it1.784
r_angle_refined_deg1.653
r_angle_other_deg1.377
r_mcbond_it1.343
r_mcbond_other1.343
r_nbd_refined0.202
r_symmetry_xyhbond_nbd_refined0.195
r_symmetry_nbd_other0.184
r_nbd_other0.178
r_nbtor_refined0.166
r_symmetry_nbd_refined0.16
r_xyhbond_nbd_refined0.146
r_chiral_restr0.089
r_symmetry_nbtor_other0.08
r_symmetry_xyhbond_nbd_other0.07
r_bond_refined_d0.01
r_gen_planes_refined0.01
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms8917
Nucleic Acid Atoms
Solvent Atoms1601
Heterogen Atoms340

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
MOLREPphasing