9IJ6

Crystal structure of the complex of erythrose-4-phosphate dehydrogenase from Acinetobacter baumannii with Adenosine phosphate at 2.40 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 MgSO4.6H2O, 0.1M HEPES sodium (pH 7.5)

Crystal Properties
Matthews coefficient	Solvent content
3.14	60.8

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 147.578	α = 90
b = 167.012	β = 90
c = 155.058	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)	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	2.4	83.646	100	0.214	0.227	0.071	0.996	7.6	9.1		74905

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	2.4	2.45	100		2.05	2.17	0.7	0.6	1	9.2

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	2.4	83.646	74868	1111	99.944	0.17	0.1696	0.2196	50.406

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]
-0.61			-4.743		5.353

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	14.672
r_dihedral_angle_6_deg	14.334
r_lrange_it	10.192
r_lrange_other	10.189
r_scangle_other	8.251
r_scangle_it	8.25
r_dihedral_angle_2_deg	7.636
r_dihedral_angle_1_deg	7.15
r_mcangle_it	5.889
r_mcangle_other	5.889
r_scbond_it	5.213
r_scbond_other	5.213
r_mcbond_it	3.962
r_mcbond_other	3.954
r_angle_refined_deg	1.527
r_angle_other_deg	0.509
r_symmetry_nbd_other	0.211
r_nbd_refined	0.204
r_nbtor_refined	0.177
r_nbd_other	0.177
r_dihedral_angle_other_2_deg	0.17
r_xyhbond_nbd_refined	0.168
r_symmetry_nbd_refined	0.132
r_symmetry_xyhbond_nbd_other	0.117
r_symmetry_xyhbond_nbd_refined	0.089
r_symmetry_nbtor_other	0.083
r_chiral_restr	0.067
r_bond_refined_d	0.006
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	10717
Nucleic Acid Atoms
Solvent Atoms	692
Heterogen Atoms	122

Software

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