8JSK | pdb_00008jsk

Crystal structure of an N-terminal cyclic nucleotide-binding domain of a PycTIR from Pseudovibrio sp. in complex with cUMP

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		277	0.075 M HEPES pH 7.5, 7.5% w/v polyethylene glycol 8,000, 6% v/v ethylene glycol and 25% v/v glycerol

Crystal Properties
Matthews coefficient	Solvent content
2.13	42.14

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 133.485	α = 90
b = 133.485	β = 90
c = 34.069	γ = 90

Symmetry
Space Group	I 4

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		2022-09-21	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSRRC BEAMLINE TPS 07A	0.97626	NSRRC	TPS 07A

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	2.401	30	99.8	1	23.6	10.5		12049

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	2.41	2.5	100		0.808	2.7	11

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	THROUGHOUT	AlphaFold	2.401	25.082	11953	664	98.826	0.2	0.1979	0.2	0.2436	0.25	37.905

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]
0.034			0.034		-0.069

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.703
r_dihedral_angle_3_deg	20.089
r_dihedral_angle_4_deg	17.812
r_dihedral_angle_1_deg	7.672
r_lrange_it	7.324
r_lrange_other	7.324
r_scangle_it	5.203
r_scangle_other	5.202
r_mcangle_it	4.297
r_mcangle_other	4.297
r_scbond_it	3.194
r_scbond_other	3.193
r_mcbond_it	2.808
r_mcbond_other	2.806
r_angle_refined_deg	1.33
r_angle_other_deg	1.149
r_symmetry_xyhbond_nbd_refined	0.218
r_nbd_refined	0.201
r_symmetry_nbd_refined	0.201
r_nbd_other	0.196
r_symmetry_nbd_other	0.193
r_xyhbond_nbd_refined	0.156
r_nbtor_refined	0.145
r_symmetry_nbtor_other	0.077
r_xyhbond_nbd_other	0.077
r_chiral_restr	0.052
r_bond_refined_d	0.007
r_gen_planes_refined	0.006
r_gen_planes_other	0.002
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2498
Nucleic Acid Atoms
Solvent Atoms	88
Heterogen Atoms	20

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
MOLREP	phasing