9QSW | pdb_00009qsw

Crystal structure of an NtA622L variant in complex with NADP+ and Nicotinic acid

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	Other		Previously solved structure with different ligand

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8.5	291	0.05 M Tris pH 8.5, 1.0 M Ammonium sulfate, 5 mM Nicotinic acid, 5 mg/ml protein (Index HT screen condition 6)

Crystal Properties
Matthews coefficient	Solvent content
2.21	44.25

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 41.026	α = 90
b = 63.353	β = 105.679
c = 61.088	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		2023-12-01	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PETRA III, DESY BEAMLINE P11	1.03272	PETRA III, DESY	P11

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	1.68	43.104	98.6	0.178	0.212	0.113	0.993	7.2	6.7		34175

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	1.68	1.7			1.685	2.006	1.073	0.536		6.6

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	1.68	43.104	33939	1763	98.517	0.182	0.1795	0.1797	0.22	0.2207	27.234

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]
1.571		0.367	-1.261		-0.446

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_other_2_deg	19.349
r_dihedral_angle_6_deg	15.04
r_dihedral_angle_3_deg	13.449
r_lrange_it	8.732
r_lrange_other	8.709
r_dihedral_angle_2_deg	8.496
r_dihedral_angle_1_deg	7.258
r_scangle_it	7.058
r_scangle_other	7.056
r_scbond_other	4.641
r_scbond_it	4.638
r_mcangle_it	4.33
r_mcangle_other	4.33
r_mcbond_it	3.009
r_mcbond_other	3.001
r_angle_refined_deg	2.186
r_angle_other_deg	0.857
r_nbd_refined	0.209
r_nbtor_refined	0.178
r_symmetry_nbd_other	0.166
r_nbd_other	0.152
r_xyhbond_nbd_refined	0.143
r_symmetry_nbd_refined	0.135
r_symmetry_xyhbond_nbd_refined	0.128
r_chiral_restr	0.119
r_symmetry_nbtor_other	0.075
r_bond_refined_d	0.013
r_gen_planes_refined	0.012
r_gen_planes_other	0.004
r_bond_other_d	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2417
Nucleic Acid Atoms
Solvent Atoms	123
Heterogen Atoms	57

Software

Software
Software Name	Purpose
REFMAC	refinement
REFMAC	refinement
Aimless	data scaling
XDS	data reduction
Coot	model building
MOLREP	phasing