7WGK | pdb_00007wgk

Crystal structure of Adenosine triphosphate phosphoribosyltransferase (HisG) from Acinetobacter baumannii at 3.13 A resolution

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5M8H

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
2.97	58.66

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 74.401	α = 90
b = 80.95	β = 90
c = 99.05	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 PILATUS 6M		2021-11-17	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID23-2	0.873	ESRF	ID23-2

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	3.13	59.49	99.8	0.109	0.999	19.4	14.9		11022			69.1

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	3.13	3.18	100		1.249	0.93	2.3	15

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	5M8H	3.13	59.488	10971	502	99.528	0.222	0.2186	0.22	0.2987	0.3	70.246

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]
-0.037			1.06		-1.023

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.693
r_dihedral_angle_3_deg	19.874
r_dihedral_angle_4_deg	16.808
r_lrange_it	15.414
r_lrange_other	15.413
r_scangle_it	8.708
r_scangle_other	8.706
r_mcangle_other	8.123
r_mcangle_it	8.122
r_dihedral_angle_1_deg	7.91
r_scbond_it	5.22
r_scbond_other	5.218
r_mcbond_it	5
r_mcbond_other	4.97
r_angle_refined_deg	1.573
r_angle_other_deg	1.186
r_symmetry_nbd_refined	0.35
r_symmetry_xyhbond_nbd_refined	0.33
r_nbd_refined	0.222
r_symmetry_nbd_other	0.205
r_nbd_other	0.182
r_xyhbond_nbd_refined	0.17
r_nbtor_refined	0.155
r_symmetry_nbtor_other	0.08
r_chiral_restr	0.065
r_symmetry_xyhbond_nbd_other	0.048
r_bond_refined_d	0.006
r_gen_planes_refined	0.005
r_gen_planes_other	0.002
r_bond_other_d	0.001

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

Software

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