9FTC | pdb_00009ftc

Aeromonas caviae CMP-Pse5Ac7Ac synthetase in the presence of CMP-Pse5Ac7Ac.

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	Other		Apo model (to be deposited)

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.5	291.15	0.2 M Sodium Nitrate; 0.1 M Bis-Tris Propane pH 6.5; 24% PEG 3350

Crystal Properties
Matthews coefficient	Solvent content
2.22	44.61

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 42.574	α = 90
b = 79.007	β = 92.46
c = 74.039	γ = 90

Symmetry
Space Group	P 1 21 1

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 X 16M		2024-03-14	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04	0.9537	Diamond	I04

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	1.5	54	99.7	0.039	0.054	0.037	0.997	15	3.5		78069

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	1.5	1.53			0.106	0.146	0.1	0.975		3.5

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	1.5	42.571	78042	4148	99.65	0.168	0.1668	0.167	0.1854	0.1851	15.153

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]
0.012		-0.16	0.814		-0.809

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	16.795
r_dihedral_angle_3_deg	12.307
r_dihedral_angle_1_deg	6.295
r_dihedral_angle_2_deg	6.154
r_lrange_it	6.11
r_lrange_other	5.927
r_scangle_it	4.089
r_scangle_other	4.088
r_dihedral_angle_other_2_deg	3.949
r_scbond_it	2.681
r_scbond_other	2.68
r_mcangle_it	2.6
r_mcangle_other	2.6
r_mcbond_it	1.756
r_mcbond_other	1.75
r_angle_refined_deg	1.729
r_angle_other_deg	0.57
r_symmetry_xyhbond_nbd_refined	0.378
r_nbd_other	0.261
r_nbd_refined	0.224
r_symmetry_nbd_refined	0.199
r_symmetry_nbd_other	0.187
r_nbtor_refined	0.186
r_xyhbond_nbd_refined	0.123
r_chiral_restr	0.086
r_symmetry_nbtor_other	0.08
r_symmetry_xyhbond_nbd_other	0.058
r_bond_refined_d	0.011
r_gen_planes_refined	0.01
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3596
Nucleic Acid Atoms
Solvent Atoms	416
Heterogen Atoms	86

Software

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