3FYO | pdb_00003fyo

Crystal structure of the triple mutant (N23C/D247E/P249A) 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	5	297	21.0 mg/mL protein mixed 1:1 with reservoir liquor containing 100 mM NaOAc (pH 5.0), 2 mM PEP, 200 microM MnSO4 and 2.0 M NaCl. Immediately prior to data collection, crystal were harvested and soaked briefly in cryoprotectant solution, comprising 20% glycerol and 100 mM NaOAc (pH 5.0) and 2.0 M NaCl, VAPOR DIFFUSION, HANGING DROP, temperature 297K

Crystal Properties
Matthews coefficient	Solvent content
2.4	48.65

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 82.74	α = 90
b = 86.197	β = 90
c = 163.891	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	110	IMAGE PLATE	RIGAKU RAXIS IV++	Osmic blue optic	2006-11-15		SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU MICROMAX-007	1.5418

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	1.8	33.95	99.5	0.065	9	4.15	108582	108582			32.4

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	1.8	1.86	100		0.472	2.3	4.09	10737

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 2QKF	1.9	33.94	92429	92429	4644	99.42	0.218	0.218	0.216	0.22	0.257	0.26	RANDOM	27.845

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]
0.6			0.25		-0.85

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.127
r_dihedral_angle_4_deg	19.389
r_dihedral_angle_3_deg	16.356
r_dihedral_angle_1_deg	6.743
r_scangle_it	5.102
r_scbond_it	3.265
r_mcangle_it	2.167
r_mcbond_it	1.306
r_angle_refined_deg	1.075
r_angle_other_deg	0.946

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.127
r_dihedral_angle_4_deg	19.389
r_dihedral_angle_3_deg	16.356
r_dihedral_angle_1_deg	6.743
r_scangle_it	5.102
r_scbond_it	3.265
r_mcangle_it	2.167
r_mcbond_it	1.306
r_angle_refined_deg	1.075
r_angle_other_deg	0.946
r_mcbond_other	0.502
r_chiral_restr	0.139
r_gen_planes_refined	0.011
r_bond_refined_d	0.01
r_gen_planes_other	0.003
r_bond_other_d

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	7886
Nucleic Acid Atoms
Solvent Atoms	453
Heterogen Atoms	14

Software

Software
Software Name	Purpose
d*TREK	data scaling
AMoRE	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
CrystalClear	data collection
d*TREK	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.