3POL | pdb_00003pol

2.3 Angstrom Crystal Structure of 3-deoxy-manno-octulosonate Cytidylyltransferase (kdsB) from Acinetobacter baumannii.

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1VH1	PDB entry 1VH1

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.5	295	Protein: 7mg/mL, 0.1M Sodium cloride, Tris-HCl (pH 8.3); Screen: Classics II (D7), 0.1M Bis-Tris pH 6.5, 25% (w/v) PEG 3350. , VAPOR DIFFUSION, SITTING DROP, temperature 295K

Crystal Properties
Matthews coefficient	Solvent content
1.97	37.7

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 107.702	α = 90
b = 40.832	β = 97.23
c = 56.491	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 225 mm CCD	Beryllium lenses	2010-11-08	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)	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	2.3	30	98.7	0.08	15.3	3.7	11015	11015		-3	39.3

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	2.3	2.34	100		0.331	4	3.7	548

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	PDB entry 1VH1	2.3	28.02	9822	9822	1073	98.68	0.18052	0.18052	0.17586	0.18	0.22275	0.22	RANDOM	35.236

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]
-0.41		2.73	-1.44		2.54

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.775
r_dihedral_angle_4_deg	15.625
r_dihedral_angle_3_deg	10.36
r_scangle_it	5.863
r_scbond_it	3.652
r_dihedral_angle_1_deg	3.017
r_mcangle_it	2.231
r_angle_refined_deg	1.489
r_mcbond_it	1.266
r_angle_other_deg	0.843

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.775
r_dihedral_angle_4_deg	15.625
r_dihedral_angle_3_deg	10.36
r_scangle_it	5.863
r_scbond_it	3.652
r_dihedral_angle_1_deg	3.017
r_mcangle_it	2.231
r_angle_refined_deg	1.489
r_mcbond_it	1.266
r_angle_other_deg	0.843
r_mcbond_other	0.339
r_chiral_restr	0.079
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	2066
Nucleic Acid Atoms
Solvent Atoms	83
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.