8YSU | pdb_00008ysu

Crystal structure of the Deinococcus wulumuqiensis CD-NTase DwCdnB in complex with CTP

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	8YSS

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		277	0.1 M BIS-TRIS propane pH 9.0, 30% w/v Polyethylene glycol 6,000.

Crystal Properties
Matthews coefficient	Solvent content
2.32	47.05

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 35.363	α = 90
b = 111.506	β = 100.415
c = 46.981	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		2022-05-26	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSRRC BEAMLINE TPS 07A	0.97624	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	1.94	30	98.2	0.995	15.424	6.5		25742

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	1.94	2.01			0.705

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	THROUGHOUT	1.944	23.881	25173	1245	95.635	0.204	0.2021	0.2087	0.2389	0.2245	26.792

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]
-0.01		0.269	-0.032		-0.053

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.034
r_dihedral_angle_3_deg	14.941
r_dihedral_angle_4_deg	13.682
r_lrange_it	8.356
r_lrange_other	8.335
r_dihedral_angle_1_deg	6.658
r_scangle_it	4.909
r_scangle_other	4.908
r_mcangle_other	3.413
r_mcangle_it	3.412
r_scbond_it	3.024
r_scbond_other	2.887
r_mcbond_it	2.207
r_mcbond_other	2.193
r_angle_refined_deg	1.444
r_angle_other_deg	1.314
r_nbd_other	0.257
r_symmetry_xyhbond_nbd_refined	0.246
r_nbd_refined	0.22
r_symmetry_nbd_other	0.192
r_xyhbond_nbd_refined	0.175
r_nbtor_refined	0.168
r_symmetry_nbd_refined	0.155
r_symmetry_nbtor_other	0.079
r_chiral_restr	0.065
r_bond_refined_d	0.009
r_gen_planes_refined	0.008
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2647
Nucleic Acid Atoms
Solvent Atoms	244
Heterogen Atoms	60

Software

Software
Software Name	Purpose
REFMAC	refinement
Blu-Ice	data collection
HKL-2000	data scaling