3C18 | pdb_00003c18

Crystal structure of nucleotidyltransferase-like protein (ZP_00538802.1) from Exiguobacterium sibiricum 255-15 at 1.90 A resolution

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8.17	277	NANODROP, 10.0% PEG 6000, 0.9M Lithium chloride, 0.1M Tris-HCl pH 8.17, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.84	56.69

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 66.74	α = 90
b = 66.74	β = 90
c = 456.2	γ = 120

Symmetry
Space Group	P 31 2 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	MARMOSAIC 325 mm CCD	Flat mirror (vertical focusing)	2007-12-05	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL11-1	0.91837, 0.97951	SSRL	BL11-1

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	29.709	99.9	0.068	9.14			95241		-3	27.097

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	1.9	1.97	99.7		0.534	2.2

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 (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MAD	THROUGHOUT	1.9	29.709	95092	4765	99.93	0.186	0.183	0.19	0.233	0.24	RANDOM	29.67

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]
0.66	0.33		0.66		-0.99

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.971
r_dihedral_angle_4_deg	14.234
r_dihedral_angle_3_deg	13.002
r_scangle_it	8.326
r_scbond_it	5.593
r_dihedral_angle_1_deg	4.453
r_mcangle_it	3.351
r_mcbond_it	1.978
r_angle_other_deg	1.418
r_angle_refined_deg	1.294

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.971
r_dihedral_angle_4_deg	14.234
r_dihedral_angle_3_deg	13.002
r_scangle_it	8.326
r_scbond_it	5.593
r_dihedral_angle_1_deg	4.453
r_mcangle_it	3.351
r_mcbond_it	1.978
r_angle_other_deg	1.418
r_angle_refined_deg	1.294
r_mcbond_other	0.553
r_chiral_restr	0.077
r_bond_refined_d	0.014
r_gen_planes_refined	0.007
r_gen_planes_other	0.002
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	7141
Nucleic Acid Atoms
Solvent Atoms	538
Heterogen Atoms	27

Software

Software
Software Name	Purpose
REFMAC	refinement
PHENIX	refinement
SOLVE	phasing
MolProbity	model building
XSCALE	data scaling
PDB_EXTRACT	data extraction
MAR345	data collection
XDS	data reduction

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.