7AA2

Chaetomium thermophilum FAD-dependent oxidoreductase in complex with ABTS


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, 20 mM MgCl2, 8.5 mM 2,2'-azino-bis(3-ethylbenzothiazoline-6-sulfonic acid), protein concentration 8 mg/ml
Crystal Properties
Matthews coefficientSolvent content
2.3647.9

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 93.589α = 90
b = 109.799β = 90
c = 115.982γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2019-06-24MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPETRA III, EMBL c/o DESY BEAMLINE P13 (MX1)0.97626PETRA III, EMBL c/o DESYP13 (MX1)

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
11.449.34395.50.0580.0670.0330.9999.23.7223121-3.716.2
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)
11.41.4299.80.9251.0790.5420.5891.43.8

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 REPLACEMENTTHROUGHOUT6ZE21.449.3432230091106695.2460.1290.12910.12770.1718random selection19.125
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]
1.996-1.229-0.767
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.582
r_dihedral_angle_4_deg20.285
r_dihedral_angle_3_deg11.971
r_dihedral_angle_1_deg7.03
r_rigid_bond_restr3.358
r_scbond_it3.13
r_scbond_other3.118
r_mcangle_other2.174
r_mcangle_it2.169
r_mcbond_it1.819
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.582
r_dihedral_angle_4_deg20.285
r_dihedral_angle_3_deg11.971
r_dihedral_angle_1_deg7.03
r_rigid_bond_restr3.358
r_scbond_it3.13
r_scbond_other3.118
r_mcangle_other2.174
r_mcangle_it2.169
r_mcbond_it1.819
r_mcbond_other1.819
r_angle_refined_deg1.751
r_angle_other_deg1.523
r_symmetry_nbd_refined0.226
r_nbd_refined0.214
r_symmetry_nbd_other0.189
r_nbd_other0.187
r_nbtor_refined0.173
r_symmetry_xyhbond_nbd_refined0.156
r_xyhbond_nbd_refined0.139
r_xyhbond_nbd_other0.122
r_chiral_restr0.106
r_symmetry_nbtor_other0.083
r_symmetry_xyhbond_nbd_other0.082
r_bond_refined_d0.013
r_gen_planes_refined0.013
r_metal_ion_refined0.004
r_bond_other_d0.002
r_gen_planes_other0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms8917
Nucleic Acid Atoms
Solvent Atoms1653
Heterogen Atoms362

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing