6ZE6

FAD-dependent oxidoreductase from Chaetomium thermophilum in complex with fragment 4-nitrocatechol

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, 20 mM MgCl2, protein concentration 8 mg/ml

Crystal Properties
Matthews coefficient	Solvent content
2.36	47.9

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 93.565	α = 90
b = 109.746	β = 90
c = 116.071	γ = 90

Symmetry
Space Group	P 21 21 21

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		2019-01-17	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	1.26	29.063	98.3	0.06	0.065	0.024	1	16.5	7.4		314691		-3.7	10

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	1.26	1.28	91		0.978	1.076	0.439	0.66	1.7	5.7

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	1.26	29.063	314581	6192	98.218	0.114	0.1144	0.11296	0.14714	random selection	14.313

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]
0.56			-0.477		-0.082

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.764
r_dihedral_angle_1_deg	19.926
r_dihedral_angle_4_deg	19.097
r_dihedral_angle_3_deg	11.108
r_rigid_bond_restr	2.779
r_scangle_other	2.573
r_scangle_it	2.572
r_lrange_other	2.484
r_scbond_it	2.212
r_scbond_other	2.205
r_angle_refined_deg	1.839
r_angle_other_deg	1.577
r_mcangle_other	1.529
r_mcangle_it	1.527
r_mcbond_it	1.246
r_mcbond_other	1.246
r_nbd_refined	0.219
r_nbd_other	0.193
r_symmetry_nbd_other	0.186
r_nbtor_refined	0.179
r_symmetry_xyhbond_nbd_refined	0.176
r_xyhbond_nbd_refined	0.152
r_symmetry_xyhbond_nbd_other	0.133
r_chiral_restr	0.118
r_symmetry_nbd_refined	0.102
r_symmetry_nbtor_other	0.09
r_bond_refined_d	0.014
r_gen_planes_refined	0.013
r_gen_planes_other	0.002
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	8917
Nucleic Acid Atoms
Solvent Atoms	1884
Heterogen Atoms	349

Software

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