8G28 | pdb_00008g28

Crystal Structure of the C-terminal Fragment of AAA ATPase from Streptococcus pneumoniae.

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	292	Protein: 5.6 mg/ml, 0.25M Sodium chloride, 0.01M Tris pH 8.3; Screen: Classics II (F12), 0.2M Sodium chloride, 0.1M HEPES pH 7.5, 25% (w/v) PEG3350.

Crystal Properties
Matthews coefficient	Solvent content
2.3	46.6

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 71.532	α = 90
b = 71.532	β = 90
c = 151.435	γ = 120

Symmetry
Space Group	P 61 2 2

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	CCD	MARMOSAIC 300 mm CCD		2021-07-28	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 21-ID-G	0.9786	APS	21-ID-G

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym 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	1.3	30	99.9	0.082	0.082	0.084	0.017	0.999	42.8	24.4		57219		-3	13.3

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.3	1.32	100		1.512	1.512	0.331	0.731	2.4	21.1

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 (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	SAD	THROUGHOUT	1.3	29.18	54123	2879	99.91	0.1213	0.1202	0.12	0.143	0.14	RANDOM	16.748

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]
-0.03	-0.02		-0.03		0.1

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	27.355
r_dihedral_angle_3_deg	10.943
r_dihedral_angle_4_deg	10.847
r_dihedral_angle_1_deg	4.337
r_angle_refined_deg	1.323
r_rigid_bond_restr	0.785
r_angle_other_deg	0.346
r_chiral_restr	0.065
r_gen_planes_refined	0.058
r_gen_planes_other	0.053

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	27.355
r_dihedral_angle_3_deg	10.943
r_dihedral_angle_4_deg	10.847
r_dihedral_angle_1_deg	4.337
r_angle_refined_deg	1.323
r_rigid_bond_restr	0.785
r_angle_other_deg	0.346
r_chiral_restr	0.065
r_gen_planes_refined	0.058
r_gen_planes_other	0.053
r_bond_refined_d	0.004
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1588
Nucleic Acid Atoms
Solvent Atoms	372
Heterogen Atoms	2

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-3000	data reduction
HKL-3000	data scaling
HKL-3000	phasing

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.