4FCU | pdb_00004fcu

1.9 Angstrom Crystal Structure of 3-deoxy-manno-octulosonate Cytidylyltransferase (kdsB) from Acinetobacter baumannii without His-Tag Bound to the Active Site

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3POL

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5.5	295	Protein: 7.4mG/mL, 0.25M Sodium cloride, Tris-HCl (pH 8.3), Screen: JCSG+ (H8), 0.2M Sodium chloride, 0.1M Bis-Tris pH 5.5, 25% (w/v) PEG 3350., VAPOR DIFFUSION, SITTING DROP, temperature 295K

Crystal Properties
Matthews coefficient	Solvent content
2.04	39.66

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 108.542	α = 90
b = 40.155	β = 103.6
c = 54.71	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	100	CCD	MARMOSAIC 300 mm CCD	Beryllium lenses	2012-02-20	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 21-ID-G	0.97856	APS	21-ID-G

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	99.8	0.091	13.3	3.7	18315	18315		-3	22

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	1.93	99.3		0.49	2.5	3.4	909

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	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	MOLECULAR REPLACEMENT	THROUGHOUT	3POL	1.9	29.52	17342	17342	940	99.78	0.18999	0.18999	0.18719	0.19	0.24233	0.25	RANDOM	22.357

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]
-0.28		1.17	-1.56		2.39

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.672
r_dihedral_angle_4_deg	12.67
r_dihedral_angle_3_deg	11.064
r_scangle_it	5.034
r_scbond_it	3.076
r_dihedral_angle_1_deg	2.945
r_mcangle_it	1.917
r_angle_refined_deg	1.415
r_mcbond_it	1.129
r_angle_other_deg	0.851

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.672
r_dihedral_angle_4_deg	12.67
r_dihedral_angle_3_deg	11.064
r_scangle_it	5.034
r_scbond_it	3.076
r_dihedral_angle_1_deg	2.945
r_mcangle_it	1.917
r_angle_refined_deg	1.415
r_mcbond_it	1.129
r_angle_other_deg	0.851
r_mcbond_other	0.345
r_chiral_restr	0.087
r_bond_refined_d	0.012
r_gen_planes_refined	0.005
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1993
Nucleic Acid Atoms
Solvent Atoms	166
Heterogen Atoms

Software

Software
Software Name	Purpose
Blu-Ice	data collection
PHASER	phasing
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling

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.