4JTI

Crystal structure of F114R/R117Q/F139G mutant of 3-deoxy-D-manno-octulosonate 8-phosphate synthase (KDO8PS) from Neisseria meningitidis

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2QKF	PDB entry 2QKF

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	4.6	297	20 mg/mL protein (in 10 mM BTP pH 7.5) mixed 1:1 with reservoir liquor containing 100 mM NaOAc (pH 4.6) and 1.6 M NaCl, cryoprotectant 20% glycerol and the reservoir solution, VAPOR DIFFUSION, HANGING DROP, temperature 297K

Crystal Properties
Matthews coefficient	Solvent content
2.33	47.19

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 81.67	α = 90
b = 85.2	β = 90
c = 162.85	γ = 90

Symmetry
Space Group	P 21 21 21

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	ADSC QUANTUM 315r		2010-11-13	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	AUSTRALIAN SYNCHROTRON BEAMLINE MX2	0.95369	Australian Synchrotron	MX2

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	1.75	40.835	100	0.088	13.6	7.2	115042	115042

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	1.75	1.84	100		0.419	0.419	1.8	7.3	16641

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB entry 2QKF	1.75	40.82	114951	5751	99.93	0.1604	0.159	0.1884	RANDOM	28.5823

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]
0.8			0.6		-1.4

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.595
r_dihedral_angle_4_deg	23.95
r_dihedral_angle_3_deg	13.525
r_dihedral_angle_1_deg	5.827
r_mcangle_it	3.316
r_mcbond_it	2.293
r_mcbond_other	2.293
r_angle_refined_deg	1.959
r_angle_other_deg	1.855
r_chiral_restr	0.113

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.595
r_dihedral_angle_4_deg	23.95
r_dihedral_angle_3_deg	13.525
r_dihedral_angle_1_deg	5.827
r_mcangle_it	3.316
r_mcbond_it	2.293
r_mcbond_other	2.293
r_angle_refined_deg	1.959
r_angle_other_deg	1.855
r_chiral_restr	0.113
r_bond_refined_d	0.021
r_bond_other_d	0.012
r_gen_planes_refined	0.012
r_gen_planes_other	0.008

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	7863
Nucleic Acid Atoms
Solvent Atoms	716
Heterogen Atoms	5

Software

Software
Software Name	Purpose
MOSFLM	data reduction
SCALA	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
ADSC	data collection

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.