6ZE7 | pdb_00006ze7

Chaetomium thermophilum FAD-dependent oxidoreductase in complex with 4-nitrophenol

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 4-nitrophenol, protein concentration 8 mg/ml

Crystal Properties
Matthews coefficient	Solvent content
2.32	47.1

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 92.611	α = 90
b = 109.674	β = 90
c = 115.634	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 6M		2017-10-05	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	BESSY BEAMLINE 14.1	0.9184	BESSY	14.1

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	1.5	47.23	99.5	0.086	0.096	0.042	0.997	10.6	5.2		186872		-3.7	11.1

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	1.5	1.53	99.2		0.908	1.008	0.429	0.668	1.7	5.3

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	6ZE2	1.5	47.23	186795	9455	99.341	0.156	0.156	0.15487	0.16	0.18162	0.16	random selection	15.971

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]
0.31			-0.739		0.429

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.14
r_dihedral_angle_4_deg	18.524
r_dihedral_angle_3_deg	12.296
r_dihedral_angle_1_deg	7.064
r_lrange_it	4.508
r_lrange_other	4.177
r_scangle_it	2.846
r_scangle_other	2.845
r_scbond_it	1.922
r_scbond_other	1.922
r_mcangle_it	1.894
r_mcangle_other	1.894
r_angle_refined_deg	1.776
r_angle_other_deg	1.478
r_mcbond_it	1.349
r_mcbond_other	1.348
r_nbd_refined	0.209
r_symmetry_nbd_other	0.187
r_nbtor_refined	0.174
r_symmetry_xyhbond_nbd_other	0.164
r_nbd_other	0.156
r_xyhbond_nbd_refined	0.152
r_symmetry_xyhbond_nbd_refined	0.146
r_metal_ion_refined	0.097
r_chiral_restr	0.095
r_symmetry_nbd_refined	0.092
r_symmetry_nbtor_other	0.084
r_bond_refined_d	0.012
r_gen_planes_refined	0.011
r_gen_planes_other	0.002
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	8923
Nucleic Acid Atoms
Solvent Atoms	1489
Heterogen Atoms	360

Software

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