8HYK

CD-NTase EfCdnE in complex with intermediate pppU[2'-5']p

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		277	sodium tartrate, PEG 3350, MgCl2, UTP

Crystal Properties
Matthews coefficient	Solvent content
2.12	42.03

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 41.418	α = 90
b = 56.94	β = 97.019
c = 64.812	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 EIGER 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)	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	2.02	30	97.8	0.067	24.5	5.9		19291

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.02	2.09	94.8		0.162		6.2

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	R-Free	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	2.021	28.486	19274	971	97.59	0.167	0.1651	0.2102	26.469

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]
0.013		-0.03	0.074		-0.077

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.833
r_dihedral_angle_4_deg	22.336
r_dihedral_angle_3_deg	14.282
r_dihedral_angle_1_deg	6.72
r_lrange_it	5.614
r_lrange_other	5.578
r_scangle_other	4.324
r_scangle_it	4.309
r_mcangle_it	3.441
r_mcangle_other	3.44
r_scbond_other	2.831
r_scbond_it	2.827
r_mcbond_it	2.383
r_mcbond_other	2.383
r_angle_refined_deg	1.453
r_angle_other_deg	1.363
r_nbd_other	0.267
r_symmetry_nbd_refined	0.218
r_nbd_refined	0.205
r_symmetry_nbd_other	0.188
r_nbtor_refined	0.176
r_symmetry_xyhbond_nbd_refined	0.167
r_symmetry_xyhbond_nbd_other	0.162
r_xyhbond_nbd_refined	0.154
r_metal_ion_refined	0.107
r_symmetry_nbtor_other	0.078
r_chiral_restr	0.072
r_bond_refined_d	0.011
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	2513
Nucleic Acid Atoms
Solvent Atoms	187
Heterogen Atoms	34

Software

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