4K3Z

Crystal structure of D-erythrulose 4-phosphate dehydrogenase from Brucella melitensis, solved by iodide SAD

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	290	EmeraldBio JCSG screen, a3: 20% PEG 3350, 200mM ammonium citrate; BrmeA.18135.a.A1.PS01411 at 20mg/ml; crystal from tray 235328a3 incubated with 500mM NaI, 20% EG in 2 steps, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 290K

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 103.5	α = 90
b = 103.5	β = 90
c = 256.54	γ = 120

Symmetry
Space Group	P 62 2 2

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	RIGAKU SATURN 944+		2012-07-06	M	SINGLE WAVELENGTH
2	2	x-ray	100	CCD	RIGAKU SATURN 944+		2012-03-30	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU	1.5418
2	ROTATING ANODE	RIGAKU	1.5418

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	1.95	50	99.7	0.09	0.09	24.13	17.2	60098	59958		-3	22.275

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	1.95	2	97.6		0.257	6.65

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (All)	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	SAD	THROUGHOUT	1.95	44.86	60098	56896	3029	99.75	0.1944	0.1927	0.2257	RANDOM	17.7039

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]
0.25	0.25		0.25		-0.81

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.343
r_dihedral_angle_4_deg	18.551
r_dihedral_angle_3_deg	13.032
r_dihedral_angle_1_deg	6.019
r_angle_refined_deg	1.366
r_angle_other_deg	0.814
r_mcangle_it	0.752
r_mcbond_it	0.442
r_mcbond_other	0.441
r_chiral_restr	0.082

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.343
r_dihedral_angle_4_deg	18.551
r_dihedral_angle_3_deg	13.032
r_dihedral_angle_1_deg	6.019
r_angle_refined_deg	1.366
r_angle_other_deg	0.814
r_mcangle_it	0.752
r_mcbond_it	0.442
r_mcbond_other	0.441
r_chiral_restr	0.082
r_bond_refined_d	0.01
r_gen_planes_refined	0.006
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4852
Nucleic Acid Atoms
Solvent Atoms	513
Heterogen Atoms	26

Software

Software
Software Name	Purpose
XSCALE	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
JDirector	data collection
XDS	data reduction

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.