7WZY | pdb_00007wzy

Crystal structure of Adenosine triphosphate phosphoribosyltransferase (HisG) from Acinetobacter baumannii at 2.975 A resolution

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	7WGM

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	4.6	298	0.1M Sodium acetate trihydrate (pH 4.6), 2M Sodium formate

Crystal Properties
Matthews coefficient	Solvent content
2.63	53.24

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 69.698	α = 90
b = 77.833	β = 90
c = 97.239	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 EIGER X 4M		2022-01-26	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE MASSIF-3	0.968	ESRF	MASSIF-3

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	2.975	60.765	90.5	0.052	0.998	8.6	4.2		6663			100.6

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.975	3.26	73.2		0.756	1.6	3

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	7WGM	2.975	60.765	6662	304	58.706	0.224	0.2205	0.22	0.2966	0.29	102.361

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]
0.72			0.174		-0.895

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.532
r_lrange_it	16.653
r_lrange_other	16.653
r_dihedral_angle_3_deg	14.798
r_dihedral_angle_4_deg	13.335
r_mcangle_it	8.738
r_mcangle_other	8.738
r_scangle_it	8.723
r_scangle_other	8.722
r_dihedral_angle_1_deg	8.167
r_mcbond_it	5.354
r_mcbond_other	5.352
r_scbond_it	5.163
r_scbond_other	5.162
r_angle_other_deg	2.233
r_angle_refined_deg	1.293
r_symmetry_nbd_refined	0.273
r_symmetry_xyhbond_nbd_refined	0.27
r_nbd_other	0.266
r_symmetry_nbd_other	0.217
r_nbd_refined	0.21
r_ncsr_local_group_1	0.154
r_nbtor_refined	0.15
r_xyhbond_nbd_refined	0.127
r_symmetry_xyhbond_nbd_other	0.07
r_symmetry_nbtor_other	0.064
r_chiral_restr	0.048
r_bond_other_d	0.034
r_gen_planes_refined	0.005
r_bond_refined_d	0.004
r_gen_planes_other	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3518
Nucleic Acid Atoms
Solvent Atoms	24
Heterogen Atoms	9

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XDS	data scaling
MOLREP	phasing