8BAS

E. coli C7 DarT1 in complex with carba-NAD and DNA

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	7OMZ

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	294	4.0 M Sodium formate, 0.1 M Tris pH 7.5

Crystal Properties
Matthews coefficient	Solvent content
4.02	69.39

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 61.903	α = 90
b = 61.903	β = 90
c = 215.547	γ = 90

Symmetry
Space Group	P 43 21 2

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 XE 16M		2022-05-26	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I03	0.976292	Diamond	I03

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	1.92	61.9	100	0.167	0.177	0.057	0.998	8.3	9.4		33191

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	1.92	1.97	100		2.472	2.606	0.818	0.501	0.9	9.8

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-Work	R-Free	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	7OMZ	1.92	59.568	33112	1660	99.943	0.172	0.1704	0.21	34.445

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]
0.617			0.617		-1.234

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	17.434
r_dihedral_angle_3_deg	13.359
r_lrange_it	9.618
r_lrange_other	9.618
r_dihedral_angle_2_deg	7.587
r_dihedral_angle_1_deg	6.765
r_scangle_it	6.565
r_scangle_other	6.563
r_scbond_other	4.727
r_scbond_it	4.726
r_mcangle_it	4.326
r_mcangle_other	4.324
r_mcbond_it	3.297
r_mcbond_other	3.297
r_angle_refined_deg	2.035
r_angle_other_deg	0.601
r_symmetry_xyhbond_nbd_refined	0.249
r_nbd_refined	0.234
r_nbd_other	0.202
r_symmetry_nbd_other	0.196
r_nbtor_refined	0.192
r_xyhbond_nbd_refined	0.187
r_symmetry_nbd_refined	0.134
r_chiral_restr	0.087
r_symmetry_nbtor_other	0.083
r_bond_refined_d	0.012
r_gen_planes_refined	0.011
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1704
Nucleic Acid Atoms	101
Solvent Atoms	242
Heterogen Atoms	76

Software

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