9S7F | pdb_00009s7f

Crystal structure of DoxA in complex with substrate DOD

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
in silico model	AlphaFold	AF-A0A2D3UDU4-F1

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5	298	0.1M Citrate pH5.0; 20% (w/v) PEG6000

Crystal Properties
Matthews coefficient	Solvent content
2.54	51.62

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 101.755	α = 90
b = 107.708	β = 90
c = 184.457	γ = 90

Symmetry
Space Group	C 2 2 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 EIGER2 S 9M		2023-04-13	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID30B	0.873	ESRF	ID30B

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	1.767	74.076	99	0.069	0.089	0.055	0.986	9.3	4.6		97832

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	1.77	1.8	94.6		1.128	1.478	0.943	0.278		4.7

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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	FREE R-VALUE	1.767	74.076	97802	4818	98.831	0.195	0.1938	0.2004	0.2223	0.2276	38.48

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]
2.413			1.189		-3.601

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	15.393
r_dihedral_angle_2_deg	13.405
r_dihedral_angle_3_deg	11.857
r_lrange_it	6.597
r_lrange_other	6.589
r_dihedral_angle_1_deg	6.192
r_scangle_it	3.578
r_scangle_other	3.578
r_scbond_it	2.353
r_scbond_other	2.353
r_angle_refined_deg	2.325
r_mcangle_it	2.172
r_mcangle_other	2.172
r_dihedral_angle_other_2_deg	2.114
r_mcbond_it	1.384
r_mcbond_other	1.384
r_angle_other_deg	0.78
r_nbd_other	0.275
r_nbd_refined	0.223
r_symmetry_nbd_refined	0.205
r_symmetry_nbd_other	0.19
r_nbtor_refined	0.182
r_symmetry_xyhbond_nbd_refined	0.172
r_xyhbond_nbd_refined	0.16
r_chiral_restr	0.113
r_symmetry_xyhbond_nbd_other	0.085
r_symmetry_nbtor_other	0.083
r_metal_ion_refined	0.076
r_bond_refined_d	0.015
r_gen_planes_refined	0.013
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6273
Nucleic Acid Atoms
Solvent Atoms	342
Heterogen Atoms	160

Software

Software
Software Name	Purpose
REFMAC	refinement
DIALS	data reduction
Aimless	data scaling
PHASER	phasing