9IIM

Structure of the complex of erythrose-4-phosphate dehydrogenase from Acinetobacter baumannii with nicotinamide adenine dinucleotide at 2.74 A resolution.

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	8ZN4

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	EVAPORATION	7.5	298	0.2M AMSO4.6H2O, 0.1M HEPES sodium (pH 7.5)

Crystal Properties
Matthews coefficient	Solvent content
3.07	59.96

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 147.262	α = 90
b = 167.618	β = 90
c = 151.58	γ = 90

Symmetry
Space Group	C 2 2 21

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	298	PIXEL	DECTRIS EIGER2 X 9M		2023-07-28	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID30B	0.87313	ESRF	ID30B

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	2.74	45.96	100	0.42	0.11	0.98	8.3	13.6		49521

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.74	2.83	100		1.98	0.56	0.61	2	13.5

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	R-Free	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	2.74	45.96	49489	1536	99.927	0.166	0.1642	0.2285	40.316

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]
1.591			-1.013		-0.577

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	13.691
r_dihedral_angle_6_deg	13.458
r_lrange_it	8.691
r_dihedral_angle_2_deg	8.683
r_lrange_other	8.678
r_dihedral_angle_1_deg	6.728
r_scangle_it	6.482
r_scangle_other	6.481
r_mcangle_other	4.619
r_mcangle_it	4.617
r_scbond_it	3.96
r_scbond_other	3.959
r_mcbond_it	2.873
r_mcbond_other	2.865
r_angle_refined_deg	1.384
r_angle_other_deg	0.487
r_nbd_other	0.302
r_symmetry_nbd_refined	0.217
r_symmetry_nbd_other	0.215
r_dihedral_angle_other_2_deg	0.213
r_nbd_refined	0.196
r_nbtor_refined	0.175
r_xyhbond_nbd_refined	0.155
r_symmetry_xyhbond_nbd_other	0.093
r_symmetry_nbtor_other	0.082
r_symmetry_xyhbond_nbd_refined	0.071
r_chiral_restr	0.065
r_bond_refined_d	0.005
r_gen_planes_refined	0.005
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	10716
Nucleic Acid Atoms
Solvent Atoms	445
Heterogen Atoms	196

Software

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