8JSJ | pdb_00008jsj

Crystal structure of an N-terminal cyclic nucleotide-binding domain of a PycTIR from Novosphingobium pentaromativorans

X-RAY DIFFRACTION

---

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	0.2 M ammonium acetate, 0.01 M calcium chloride dihydrate,0.05 M sodium cacodylate trihydrate pH 6.5,10% w/v polyethylene glycol 4,000

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 87.115	α = 90
b = 87.115	β = 90
c = 93.349	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 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	2.858	30	99.8	0.998	85	34.5		5229

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	2.86	2.96	100		0.895	2.7

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	2.858	24.345	4901	247	93.817	0.259	0.2578	0.26	0.282	0.32	53.472

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]
-0.041	-0.021		-0.041		0.134

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.882
r_dihedral_angle_3_deg	22.793
r_dihedral_angle_4_deg	19.384
r_lrange_other	12.761
r_lrange_it	12.706
r_dihedral_angle_1_deg	8.969
r_scangle_it	7.749
r_scangle_other	7.743
r_mcangle_other	6.89
r_mcangle_it	6.882
r_scbond_it	4.801
r_scbond_other	4.798
r_mcbond_it	4.218
r_mcbond_other	4.208
r_angle_refined_deg	1.451
r_angle_other_deg	1.135
r_symmetry_nbd_refined	0.282
r_nbd_other	0.246
r_nbd_refined	0.245
r_symmetry_nbd_other	0.224
r_symmetry_xyhbond_nbd_refined	0.208
r_xyhbond_nbd_refined	0.204
r_nbtor_refined	0.156
r_symmetry_nbtor_other	0.085
r_symmetry_xyhbond_nbd_other	0.065
r_chiral_restr	0.047
r_bond_refined_d	0.01
r_gen_planes_refined	0.007
r_bond_other_d	0.003
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1017
Nucleic Acid Atoms
Solvent Atoms	50
Heterogen Atoms

Software

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