8YSR | pdb_00008ysr

Crystal structure of the Deinococcus wulumuqiensis CD-NTase DwCdnB in complex with hexatungstotellurate(VI) TEW

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		277	0.2 M Ammonium acetate, 0.1 M Tris pH 8.0, 16% w/v Polyethylene glycol 10,000.

Crystal Properties
Matthews coefficient	Solvent content
2.35	47.57

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 35.367	α = 100.48
b = 46.798	β = 104.89
c = 60.374	γ = 100.13

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 9M		2021-03-26	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSRRC BEAMLINE TPS 05A	1.21366	NSRRC	TPS 05A

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	2.04	30	96.9	0.1	24.636	6.5		21801

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	2.04	2.12			0.983

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 (Observed)	R-Work (Depositor)	R-Free (Depositor)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	SAD	THROUGHOUT	2.04	25.58	19654	1983	95.15	0.18402	0.18083	0.21548	RANDOM	30.573

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]
-1.28	0.13	0.08	-0.59	-2.48	2.58

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.363
r_dihedral_angle_3_deg	14.918
r_dihedral_angle_4_deg	14.309
r_long_range_B_refined	7.664
r_long_range_B_other	7.402
r_dihedral_angle_1_deg	6.194
r_scangle_other	5.814
r_mcangle_it	4.095
r_mcangle_other	4.094
r_scbond_it	3.836
r_scbond_other	3.593
r_mcbond_other	2.748
r_mcbond_it	2.747
r_angle_other_deg	1.553
r_angle_refined_deg	1.397
r_chiral_restr	0.066
r_bond_refined_d	0.01
r_gen_planes_refined	0.006
r_bond_other_d	0.002
r_gen_planes_other	0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2654
Nucleic Acid Atoms
Solvent Atoms	265
Heterogen Atoms	31

Software

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