8BAQ | pdb_00008baq

E. coli C7 DarT1 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	7OMW

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5.5	294	4.0M Sodium Formate, 0.1M Sodium Acetate pH 5.5

Crystal Properties
Matthews coefficient	Solvent content
2.62	53.06

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 62.308	α = 90
b = 62.308	β = 90
c = 113.081	γ = 120

Symmetry
Space Group	P 31 2 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 XE 16M		2022-02-24	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I03	0.976254	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	2	54.018	99.9	0.115	0.143	0.084	0.997	5.8	4.4		17764

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	2	2.05	99.9		1.223	1.527	0.723	0.615	0.7	4.4

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	FREE R-VALUE	7OMW	2	54.018	17726	792	99.73	0.198	0.1957	0.2	0.2483	0.27	42.664

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]
0.952	0.476		0.952		-3.089

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	15.959
r_dihedral_angle_3_deg	13.151
r_dihedral_angle_1_deg	6.571
r_lrange_it	6.294
r_dihedral_angle_2_deg	6.288
r_lrange_other	6.254
r_scangle_it	3.848
r_scangle_other	3.846
r_mcangle_other	3.434
r_mcangle_it	3.433
r_scbond_it	2.392
r_scbond_other	2.391
r_mcbond_it	2.197
r_mcbond_other	2.19
r_angle_refined_deg	1.171
r_angle_other_deg	0.375
r_nbd_other	0.214
r_nbd_refined	0.205
r_xyhbond_nbd_refined	0.191
r_symmetry_nbd_other	0.19
r_symmetry_nbd_refined	0.189
r_nbtor_refined	0.182
r_symmetry_xyhbond_nbd_refined	0.174
r_symmetry_nbtor_other	0.078
r_chiral_restr	0.053
r_symmetry_xyhbond_nbd_other	0.025
r_gen_planes_refined	0.005
r_bond_refined_d	0.004
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
Solvent Atoms	131
Heterogen Atoms	60

Software

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