6ZE3

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

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6ZE2

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5.5	293.15	17 % (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 coefficient	Solvent content
2.34	47.5

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 109.683	α = 90
b = 115.585	β = 90
c = 46.605	γ = 90

Symmetry
Space Group	P 21 21 2

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	PIXEL	DECTRIS PILATUS 2M		2019-05-15	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	BESSY BEAMLINE 14.2	0.9184	BESSY	14.2

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)	Redundancy	Number Reflections (All)	Number Reflections (Observed)	Observed Criterion Sigma (F)	Observed Criterion Sigma (I)	B (Isotropic) From Wilson Plot
1	2.22	43.261	99.9	0.167	0.18	0.066	0.996	8.3	7.3		30083		-3.7	33.5

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)	Redundancy	Number Unique Reflections (All)
1	2.22	2.29	100		1.147	1.23	0.441	0.646	1.8	7.7

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	6ZE2	2.22	43.261	30028	1503	99.834	0.18	0.1798	0.17828	0.25488	random selection	41.298

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			-1.162		2.815

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.535
r_dihedral_angle_4_deg	17.053
r_dihedral_angle_3_deg	13.275
r_dihedral_angle_1_deg	8.139
r_lrange_it	7.335
r_lrange_other	7.327
r_scangle_it	5.594
r_scangle_other	5.593
r_mcangle_it	5.14
r_mcangle_other	5.14
r_scbond_it	3.838
r_scbond_other	3.835
r_mcbond_it	3.692
r_mcbond_other	3.691
r_angle_refined_deg	1.738
r_angle_other_deg	1.296
r_nbd_other	0.269
r_symmetry_xyhbond_nbd_refined	0.199
r_symmetry_nbd_refined	0.197
r_nbd_refined	0.196
r_symmetry_nbd_other	0.196
r_xyhbond_nbd_refined	0.169
r_nbtor_refined	0.163
r_symmetry_nbtor_other	0.077
r_chiral_restr	0.074
r_symmetry_xyhbond_nbd_other	0.054
r_bond_refined_d	0.01
r_gen_planes_refined	0.008
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4461
Nucleic Acid Atoms
Solvent Atoms	310
Heterogen Atoms	154

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XDS	data scaling
MOLREP	phasing