8YSM | pdb_00008ysm

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

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	Other		apo DwCdnB

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
2.47	50.15

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 35.401	α = 105.45
b = 46.765	β = 103.349
c = 64.182	γ = 99.327

Symmetry
Space Group	P 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		2022-06-20	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)	R Merge I (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	1.5	30	96.7	0.044	1	40.4	6.8		57942

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	1.5	1.55			0.978

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	1.5	23.508	57636	2791	96.001	0.174	0.1734	0.1737	0.1927	0.1927	19.78

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]
-0.015	-0.033	0.042	-0.021	-0.152	0.102

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.48
r_dihedral_angle_4_deg	13.974
r_dihedral_angle_3_deg	13.074
r_dihedral_angle_1_deg	6.528
r_lrange_it	5.975
r_lrange_other	5.799
r_scangle_it	4.453
r_scangle_other	4.432
r_mcangle_it	3.211
r_mcangle_other	3.21
r_scbond_it	2.88
r_scbond_other	2.864
r_mcbond_it	2.142
r_mcbond_other	2.142
r_angle_refined_deg	1.445
r_angle_other_deg	1.408
r_nbd_other	0.29
r_nbd_refined	0.214
r_symmetry_nbd_other	0.188
r_symmetry_nbd_refined	0.185
r_nbtor_refined	0.174
r_symmetry_xyhbond_nbd_refined	0.171
r_xyhbond_nbd_refined	0.166
r_chiral_restr	0.082
r_symmetry_nbtor_other	0.08
r_xyhbond_nbd_other	0.041
r_bond_refined_d	0.014
r_gen_planes_refined	0.012
r_gen_planes_other	0.002
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2647
Nucleic Acid Atoms
Solvent Atoms	378
Heterogen Atoms	36

Software

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