6DT3 | pdb_00006dt3

1.2 Angstrom Resolution Crystal Structure of Nucleoside Triphosphatase NudI from Klebsiella pneumoniae in Complex with HEPES

X-RAY DIFFRACTION

---

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	292	10.0 mg/mL protein, 0.5 M sodium chloride, 0.01 M Tris, pH 8.3 against Classics II (F8) (0.2 M ammonium sulfate, 0.1 M HEPES, pH 7.5, 25% w/v PEG3350)

Crystal Properties
Matthews coefficient	Solvent content
2.18	43.6

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 33.14	α = 77.07
b = 39.346	β = 80.74
c = 56.294	γ = 86.2

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	CCD	RAYONIX MX-300	C(111)	2018-04-11	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 21-ID-F	0.97872	APS	21-ID-F

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym I (Observed)	Rrim I (All)	Rpim I (All)	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	1.2	30	92.3	0.07	0.07	0.088	0.052	13.7	2.8		78810		-3	12.3

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.2	1.22	91.1		0.79	0.79	0.973	0.563	0.593	2.1	2.9

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-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	SAD	THROUGHOUT	1.2	27.14	74887	3897	92.16	0.15503	0.1534	0.15	0.18662	0.19	RANDOM	16.812

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]
0.05	0.61	-0.47	0.66		-0.68

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	27.156
r_sphericity_free	16.896
r_rigid_bond_restr	11.074
r_dihedral_angle_4_deg	10.724
r_dihedral_angle_3_deg	10.458
r_sphericity_bonded	7.487
r_dihedral_angle_1_deg	5.562
r_long_range_B_refined	2.807
r_long_range_B_other	2.806
r_scangle_other	2.288
r_scbond_it	2
r_scbond_other	1.985
r_mcangle_it	1.614
r_mcangle_other	1.614
r_angle_refined_deg	1.4
r_mcbond_it	1.38
r_mcbond_other	1.374
r_angle_other_deg	0.505
r_chiral_restr	0.077
r_gen_planes_refined	0.04
r_gen_planes_other	0.037
r_bond_refined_d	0.008
r_bond_other_d	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

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2312
Nucleic Acid Atoms
Solvent Atoms	343
Heterogen Atoms	15

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling
HKL-3000	phasing