6ZE3

FAD-dependent oxidoreductase from Chaetomium thermophilum in complex with fragment (4-methoxycarbonylphenyl)methylazanium


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
2.3447.5

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 109.683α = 90
b = 115.585β = 90
c = 46.605γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 2M2019-05-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONBESSY BEAMLINE 14.20.9184BESSY14.2

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
12.2243.26199.90.1670.180.0660.9968.37.330083-3.733.5
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)
12.222.291001.1471.230.4410.6461.87.7

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 REPLACEMENTTHROUGHOUT6ZE22.2243.26130028150399.8340.180.17980.178280.25488random selection41.298
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]
-1.653-1.1622.815
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.535
r_dihedral_angle_4_deg17.053
r_dihedral_angle_3_deg13.275
r_dihedral_angle_1_deg8.139
r_lrange_it7.335
r_lrange_other7.327
r_scangle_it5.594
r_scangle_other5.593
r_mcangle_it5.14
r_mcangle_other5.14
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.535
r_dihedral_angle_4_deg17.053
r_dihedral_angle_3_deg13.275
r_dihedral_angle_1_deg8.139
r_lrange_it7.335
r_lrange_other7.327
r_scangle_it5.594
r_scangle_other5.593
r_mcangle_it5.14
r_mcangle_other5.14
r_scbond_it3.838
r_scbond_other3.835
r_mcbond_it3.692
r_mcbond_other3.691
r_angle_refined_deg1.738
r_angle_other_deg1.296
r_nbd_other0.269
r_symmetry_xyhbond_nbd_refined0.199
r_symmetry_nbd_refined0.197
r_nbd_refined0.196
r_symmetry_nbd_other0.196
r_xyhbond_nbd_refined0.169
r_nbtor_refined0.163
r_symmetry_nbtor_other0.077
r_chiral_restr0.074
r_symmetry_xyhbond_nbd_other0.054
r_bond_refined_d0.01
r_gen_planes_refined0.008
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4461
Nucleic Acid Atoms
Solvent Atoms310
Heterogen Atoms154

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
MOLREPphasing