7OUD | pdb_00007oud

Crystal structure of a ternary complex of the flavoprotein monooxygenase GrhO5 with FAD and collinone

X-RAY DIFFRACTION

---

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
other		RubL

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	295	20 % PEG 3350, 200mM di-sodium malonate

Crystal Properties
Matthews coefficient	Solvent content
2.82	56.36

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 45.666	α = 90
b = 103.747	β = 104.594
c = 69.005	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 EIGER X 16M		2020-09-11	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X06SA	1.0	SLS	X06SA

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	2.3	44.19	97	0.2	0.92	5.8	3.2		26914

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.3	2.42			0.49	0.83

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-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	NONE	RubL	2.3	44.19	26882	1392	97.156	0.227	0.225	0.23	0.2629	0.26	9.322

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]
0.043		-0.002	0.015		-0.05

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	29.358
r_dihedral_angle_4_deg	17.626
r_dihedral_angle_3_deg	15.785
r_dihedral_angle_1_deg	7.473
r_lrange_it	3.421
r_lrange_other	3.348
r_mcangle_it	1.646
r_mcangle_other	1.646
r_scangle_it	1.597
r_scangle_other	1.597
r_angle_refined_deg	1.543
r_angle_other_deg	1.295
r_mcbond_it	0.913
r_mcbond_other	0.913
r_scbond_it	0.893
r_scbond_other	0.892
r_symmetry_xyhbond_nbd_refined	0.225
r_nbd_other	0.209
r_nbd_refined	0.198
r_symmetry_nbd_other	0.193
r_nbtor_refined	0.16
r_xyhbond_nbd_refined	0.156
r_symmetry_nbd_refined	0.132
r_symmetry_nbtor_other	0.079
r_symmetry_xyhbond_nbd_other	0.078
r_chiral_restr	0.071
r_bond_refined_d	0.009
r_gen_planes_refined	0.006
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3885
Nucleic Acid Atoms
Solvent Atoms	278
Heterogen Atoms	92

Software

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