9QWY | pdb_00009qwy

Crystal structure of an NtA622L variant in complex with NADPH and Trigonelline

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 a different ligand

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.5	291	5 mg/ml Protein, 1 mM Trigonelline, 0.5 mM NADPH, 0.1 M Sodium chloride, 0.05 M BIS-TRIS, 12.5% PEG 3350, 500x diluted seed stock

Crystal Properties
Matthews coefficient	Solvent content
2.34	47.39

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 66.227	α = 90
b = 64.917	β = 101.513
c = 115.352	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 EIGER X 9M		2024-04-18	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID23-2	0.87313	ESRF	ID23-2

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	2.6	64.92	97.8	0.267	0.377	0.266	0.615	5.9	3.3		29126

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	2.6	2.72			1.026	1.449	1.023	0.436		3.5

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	2.6	56.293	29110	1471	97.609	0.209	0.2062	0.2078	0.2678	0.2699	60.844

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]
-2.908		1.836	1.061		1.015

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	18.261
r_dihedral_angle_2_deg	16.29
r_dihedral_angle_6_deg	15.411
r_dihedral_angle_1_deg	7.772
r_dihedral_angle_other_2_deg	7.59
r_lrange_it	7.512
r_lrange_other	7.512
r_scangle_it	3.316
r_scangle_other	3.316
r_mcangle_it	2.976
r_mcangle_other	2.976
r_angle_refined_deg	2.671
r_scbond_it	2.044
r_scbond_other	2.043
r_mcbond_it	1.822
r_mcbond_other	1.822
r_angle_other_deg	0.954
r_symmetry_xyhbond_nbd_refined	0.322
r_symmetry_nbd_refined	0.272
r_nbd_refined	0.21
r_nbtor_refined	0.178
r_xyhbond_nbd_refined	0.175
r_nbd_other	0.174
r_symmetry_nbd_other	0.17
r_chiral_restr	0.13
r_ncsr_local_group_1	0.126
r_ncsr_local_group_3	0.123
r_ncsr_local_group_2	0.117
r_symmetry_nbtor_other	0.082
r_bond_refined_d	0.015
r_gen_planes_refined	0.012
r_bond_other_d	0.003
r_gen_planes_other	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	7251
Nucleic Acid Atoms
Solvent Atoms	105
Heterogen Atoms	174

Software

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