9QRG | pdb_00009qrg

Crystal structure of mutant NtA622L in complex with NADP+ and Nicotinamide

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	Other		A previously solved lower resolution structure

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		291	3.75 mg/ml purified A119, 0.1 M Sodium formate, 10% w/v Polyethylene glycol 3,350 (Index HT Screen condition 90)

Crystal Properties
Matthews coefficient	Solvent content
2.11	41.83

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 43.289	α = 90
b = 47.459	β = 90
c = 142.623	γ = 90

Symmetry
Space Group	P 21 21 21

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		2022-11-22	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PETRA III, DESY BEAMLINE P11	1.03323	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	1.3	47.46	87.8	0.028	0.033	0.017	0.999	26.6	6.4		64136

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			0.762	0.94	0.542	0.604		4.3

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	1.3	45.031	64093	3070	87.443	0.135	0.1335	0.1335	0.1682	0.168	25.242

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]
0.186			-0.12		-0.066

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_other_2_deg	25.816
r_lrange_it	20.191
r_lrange_other	18.548
r_dihedral_angle_6_deg	15.939
r_dihedral_angle_3_deg	13.006
r_scangle_it	11.983
r_scangle_other	11.98
r_mcangle_other	9.075
r_mcangle_it	9.06
r_scbond_it	8.631
r_scbond_other	8.628
r_dihedral_angle_2_deg	8.382
r_mcbond_it	6.634
r_mcbond_other	6.548
r_dihedral_angle_1_deg	6.291
r_rigid_bond_restr	3.966
r_angle_refined_deg	1.91
r_angle_other_deg	0.806
r_xyhbond_nbd_refined	0.234
r_nbd_refined	0.223
r_nbd_other	0.193
r_nbtor_refined	0.18
r_symmetry_nbd_other	0.178
r_symmetry_xyhbond_nbd_refined	0.151
r_symmetry_nbd_refined	0.142
r_chiral_restr	0.109
r_symmetry_nbtor_other	0.074
r_bond_refined_d	0.011
r_gen_planes_refined	0.011
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	254
Heterogen Atoms	59

Software

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