7OMW

Thermus sp. 2.9 DarT in complex with NAD+

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	7OMV	D_1292116023

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		294	50 mM potassium thiocyanate, 20% (w/v) PEG2000MME

Crystal Properties
Matthews coefficient	Solvent content
2.28	45.95

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 36.032	α = 90
b = 61.745	β = 95.198
c = 50.197	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 EIGER2 X 16M		2019-07-08	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04	0.9795	Diamond	I04

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	1.3	35.909	97	0.041	0.045	0.017	0.999	20.3	5.9		52232

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	1.3	1.32			0.227	0.277	0.155	0.949	3.5

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	D_1292116023	1.3	35.909	52208	2518	96.899	0.132	0.131	0.1525	17.786

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]
1.524		-2.648	-0.37		-0.662

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	29.894
r_dihedral_angle_4_deg	19
r_dihedral_angle_3_deg	13.326
r_rigid_bond_restr	7.617
r_dihedral_angle_1_deg	6.76
r_lrange_it	4.176
r_scangle_it	3.827
r_lrange_other	3.817
r_scangle_other	3.811
r_scbond_it	3.083
r_scbond_other	3.039
r_mcangle_it	2.221
r_mcangle_other	2.22
r_mcbond_it	1.817
r_mcbond_other	1.816
r_angle_refined_deg	1.803
r_angle_other_deg	1.45
r_symmetry_nbd_refined	0.353
r_nbd_refined	0.273
r_symmetry_xyhbond_nbd_refined	0.272
r_nbd_other	0.221
r_symmetry_nbd_other	0.188
r_nbtor_refined	0.182
r_xyhbond_nbd_refined	0.127
r_chiral_restr	0.105
r_symmetry_nbtor_other	0.086
r_symmetry_xyhbond_nbd_other	0.024
r_bond_refined_d	0.013
r_gen_planes_refined	0.011
r_bond_other_d	0.002
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1627
Nucleic Acid Atoms
Solvent Atoms	175
Heterogen Atoms	65

Software

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