8ZN4 | pdb_00008zn4

Crystal structure of Poly(ethylene glycol) stabilized erythrose-4-phosphate dehydrogenase from Acinetobacter baumannii at 2.30 A resolution

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3CMC

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	59.04

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 145.775	α = 90
b = 167.135	β = 90
c = 150.103	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	2.3	46.703	100	0.2	0.02	0.06	0.998	11.2	13.2		81357

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	2.3	2.34	100		1.58	1.69	0.47	0.82	2.2	12.6

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	3CMC	2.3	46.703	81321	2400	99.963	0.153	0.1517	0.16	0.201	0.2	44.028

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]
1.561			-3.614		2.053

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	14.571
r_dihedral_angle_3_deg	13.205
r_lrange_it	9.593
r_lrange_other	9.584
r_dihedral_angle_2_deg	8.827
r_scangle_it	7.528
r_scangle_other	7.528
r_dihedral_angle_1_deg	7.008
r_mcangle_it	5.144
r_mcangle_other	5.143
r_scbond_it	4.988
r_scbond_other	4.988
r_mcbond_it	3.591
r_mcbond_other	3.59
r_angle_refined_deg	1.547
r_angle_other_deg	0.52
r_metal_ion_refined	0.259
r_dihedral_angle_other_2_deg	0.241
r_symmetry_nbd_other	0.214
r_nbd_other	0.203
r_nbd_refined	0.201
r_symmetry_nbd_refined	0.184
r_nbtor_refined	0.176
r_symmetry_xyhbond_nbd_refined	0.171
r_xyhbond_nbd_refined	0.162
r_symmetry_nbtor_other	0.085
r_chiral_restr	0.071
r_symmetry_xyhbond_nbd_other	0.023
r_bond_refined_d	0.007
r_gen_planes_refined	0.007
r_bond_other_d	0.005
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	10716
Nucleic Acid Atoms
Solvent Atoms	641
Heterogen Atoms	488

Software

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