9FTB | pdb_00009ftb

Aeromonas caviae CMP-Pse5A7Ac Synthetase

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
in silico model	AlphaFold	Q2M5Q2

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		291	1% w/v Tryptone, 0.05 M HEPES sodium pH 6.5, 14% w/v PEG3350, 0.001 M sodium azide

Crystal Properties
Matthews coefficient	Solvent content
2.69	54.29

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 109.527	α = 90
b = 109.527	β = 90
c = 87.063	γ = 120

Symmetry
Space Group	P 65 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	PIXEL	DECTRIS EIGER2 S 16M		2022-05-27	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I03	0.976	Diamond	I03

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	1.9	64.223	100	0.218	0.223	0.048	0.999	14.8	40		24845

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	1.9	1.94			4.346	4.447	0.943	0.917		41.8

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 (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	1.9	64.223	24803	1187	99.984	0.194	0.1916	0.1899	0.2406	0.2361	39.633

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]
0.476	0.238		0.476		-1.544

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	17.79
r_dihedral_angle_3_deg	15.513
r_lrange_it	7.733
r_lrange_other	7.71
r_dihedral_angle_1_deg	7.106
r_dihedral_angle_2_deg	6.83
r_scangle_it	5.824
r_scangle_other	5.822
r_mcangle_it	4.124
r_mcangle_other	4.123
r_scbond_it	4.037
r_scbond_other	4.035
r_mcbond_it	3.008
r_mcbond_other	3.008
r_angle_refined_deg	2.174
r_angle_other_deg	0.717
r_nbd_refined	0.226
r_symmetry_nbd_other	0.209
r_nbtor_refined	0.193
r_nbd_other	0.183
r_xyhbond_nbd_refined	0.18
r_chiral_restr	0.108
r_symmetry_xyhbond_nbd_refined	0.107
r_symmetry_nbtor_other	0.09
r_symmetry_nbd_refined	0.08
r_symmetry_xyhbond_nbd_other	0.047
r_bond_refined_d	0.016
r_gen_planes_refined	0.014
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1827
Nucleic Acid Atoms
Solvent Atoms	133
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
Aimless	data scaling
PHASER	phasing
XDS	data reduction