8ZN1

Structure of erythrose-4-phosphate dehydrogenase from Acinetobacter baumannii at 3.00 A resolution

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	EVAPORATION	7.5	298	A reservoir solution containing 0.2 M MgCl2.6H2O, 0.1 M HEPES sodium (pH 7.5), and 30% v/v PEG 400 was prepared.

Crystal Properties
Matthews coefficient	Solvent content
3.1	60.31

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 147.646	α = 90
b = 167.88	β = 90
c = 152.269	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	3	49.536	100	0.73	0.79	0.21	0.971	7.3	13.5		38162

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	3	3.13	100		2.86	2.98	0.78	0.69	1.9	14.4

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	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	3CMC	3	49.536	38116	754	99.893	0.167	0.1658	0.2419	48.146

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]
-0.227			-3.798		4.025

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	14.348
r_dihedral_angle_6_deg	13.206
r_lrange_it	9.201
r_lrange_other	9.2
r_dihedral_angle_2_deg	8.761
r_dihedral_angle_1_deg	6.871
r_scangle_it	6.858
r_scangle_other	6.845
r_mcangle_it	5.405
r_mcangle_other	5.405
r_scbond_it	4.209
r_scbond_other	4.2
r_mcbond_it	3.379
r_mcbond_other	3.377
r_angle_refined_deg	1.499
r_angle_other_deg	0.506
r_dihedral_angle_other_2_deg	0.435
r_nbd_other	0.349
r_symmetry_nbd_other	0.212
r_nbd_refined	0.209
r_nbtor_refined	0.18
r_symmetry_nbd_refined	0.169
r_xyhbond_nbd_refined	0.167
r_symmetry_nbtor_other	0.083
r_chiral_restr	0.065
r_symmetry_xyhbond_nbd_other	0.031
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	10716
Nucleic Acid Atoms
Solvent Atoms	265
Heterogen Atoms	216

Software

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