3EWI | pdb_00003ewi

Structural analysis of the C-terminal domain of murine CMP-Sialic acid Synthetase

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8	277	EtOH, Tris, DTT, Neu5Ac, pH 8, vapor diffusion, sitting drop, temperature 277K
2	VAPOR DIFFUSION, SITTING DROP	7.5	277	EtOH, Tris, DTT, Neu5Ac, pH 7.5, vapor diffusion, sitting drop, temperature 277K

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 121.09	α = 90
b = 37.49	β = 116.3
c = 78.83	γ = 90

Symmetry
Space Group	C 1 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		CCD	MAR CCD 165 mm		2007-06-14	M	SINGLE WAVELENGTH
2	1	x-ray		CCD	MARMOSAIC 225 mm CCD		2007-08-01	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	BESSY BEAMLINE 14.2	0.9184	BESSY	14.2
2	SYNCHROTRON	BESSY BEAMLINE 14.1	0.9797, 0.9799, 0.9117	BESSY	14.1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym 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	1.9	27.43	95.6	0.042	0.042	27.636	4.2		24430

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	1.9	1.97	69.5		0.252	0.252	3.4	2.7	1769

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		THROUGHOUT	1.9	27.43	24429	1256	95.2	0.209	0.206	0.28	0.25	0.3	RANDOM	24.153

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]
0.03		0.62	-0.53		1.05

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.98
r_dihedral_angle_3_deg	15.789
r_dihedral_angle_4_deg	14.499
r_dihedral_angle_1_deg	6.676
r_angle_refined_deg	1.304
r_nbtor_refined	0.296
r_symmetry_vdw_refined	0.227
r_nbd_refined	0.207
r_symmetry_hbond_refined	0.194
r_xyhbond_nbd_refined	0.17

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.98
r_dihedral_angle_3_deg	15.789
r_dihedral_angle_4_deg	14.499
r_dihedral_angle_1_deg	6.676
r_angle_refined_deg	1.304
r_nbtor_refined	0.296
r_symmetry_vdw_refined	0.227
r_nbd_refined	0.207
r_symmetry_hbond_refined	0.194
r_xyhbond_nbd_refined	0.17
r_chiral_restr	0.092
r_bond_refined_d	0.014
r_gen_planes_refined	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2394
Nucleic Acid Atoms
Solvent Atoms	181
Heterogen Atoms

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data collection
HKL-2000	data reduction
HKL-2000	data scaling
DM	phasing

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.