6ZE2

FAD-dependent oxidoreductase from Chaetomium thermophilum

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4YNT

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 cystamine, protein concentration 8 mg/ml

Crystal Properties
Matthews coefficient	Solvent content
2.37	48.1

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 46.654	α = 90
b = 116.774	β = 90.797
c = 109.903	γ = 90

Symmetry
Space Group	P 1 21 1

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 6M		2016-10-21	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PETRA III, EMBL c/o DESY BEAMLINE P13 (MX1)	1.0332	PETRA III, EMBL c/o DESY	P13 (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)	Redundancy	Number Reflections (All)	Number Reflections (Observed)	Observed Criterion Sigma (F)	Observed Criterion Sigma (I)	B (Isotropic) From Wilson Plot
1	1.31	46.69	95.4	0.045	0.053	0.029	0.999	11.2	3.2		268173		-3.7	12.7

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	1.31	1.33	96.8		0.489	0.599	0.34	0.795	2	2.8

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	4YNT	1.31	46.69	268125	5346	95.348	0.107	0.1072	0.1059	0.11	0.137	0.12	random selection	17.369

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]
0.568		0.293	0.335		-0.91

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.992
r_dihedral_angle_4_deg	18.812
r_dihedral_angle_3_deg	11.281
r_dihedral_angle_1_deg	6.958
r_rigid_bond_restr	3.354
r_lrange_it	3.215
r_scangle_it	2.907
r_scangle_other	2.907
r_lrange_other	2.871
r_scbond_it	2.541
r_scbond_other	2.541
r_mcangle_other	2.009
r_mcangle_it	2.007
r_angle_refined_deg	1.825
r_mcbond_it	1.655
r_mcbond_other	1.655
r_angle_other_deg	1.572
r_nbd_refined	0.219
r_nbd_other	0.211
r_symmetry_xyhbond_nbd_refined	0.192
r_symmetry_nbd_other	0.191
r_symmetry_nbd_refined	0.179
r_nbtor_refined	0.177
r_xyhbond_nbd_refined	0.138
r_chiral_restr	0.109
r_symmetry_nbtor_other	0.085
r_symmetry_xyhbond_nbd_other	0.061
r_bond_refined_d	0.013
r_gen_planes_refined	0.013
r_bond_other_d	0.002
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	8922
Nucleic Acid Atoms
Solvent Atoms	1664
Heterogen Atoms	267

Software

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