8YSJ | pdb_00008ysj

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

X-RAY DIFFRACTION

---

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 pH6.5, 20 % w/v PEG 5000 MME.

Crystal Properties
Matthews coefficient	Solvent content
2.34	47.54

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 35.346	α = 74.396
b = 46.244	β = 73.126
c = 61.058	γ = 84.271

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		2021-10-27	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSRRC BEAMLINE TPS 05A	0.99984	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	1.9	30	95	0.024	32.553	2.1		26385

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	1.9	1.97			0.972

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	1.903	28.287	26372	1381	94.263	0.173	0.1708	0.1818	0.2074	0.213	25.599

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]
0.163	-0.182	0.053	-0.079	0.127	-0.022

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.597
r_dihedral_angle_3_deg	15.068
r_dihedral_angle_4_deg	14.985
r_lrange_it	7.963
r_lrange_other	7.443
r_dihedral_angle_1_deg	6.68
r_scangle_it	5.34
r_scangle_other	4.569
r_mcangle_it	3.527
r_mcangle_other	3.526
r_scbond_it	3.401
r_scbond_other	2.945
r_mcbond_it	2.415
r_mcbond_other	2.415
r_angle_refined_deg	1.431
r_angle_other_deg	1.338
r_nbd_refined	0.211
r_nbd_other	0.185
r_symmetry_nbd_other	0.182
r_nbtor_refined	0.173
r_symmetry_nbd_refined	0.173
r_symmetry_xyhbond_nbd_refined	0.163
r_xyhbond_nbd_refined	0.158
r_symmetry_nbtor_other	0.078
r_chiral_restr	0.073
r_symmetry_xyhbond_nbd_other	0.013
r_bond_refined_d	0.01
r_gen_planes_refined	0.009
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2616
Nucleic Acid Atoms
Solvent Atoms	234
Heterogen Atoms	58

Software

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