3UPY

Crystal structure of the Brucella abortus enzyme catalyzing the first committed step of the methylerythritol 4-phosphate pathway.

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3UPL	pdb entry 3UPL

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7	293	14-20% PEG4000, 0.1M HEPES, 0.2M magnesium chloride, 0.5 mM fosmidomycin , pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.28	46.11

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 49.391	α = 68.79
b = 63.379	β = 75.54
c = 79.334	γ = 72.07

Symmetry
Space Group	P 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	mirrors	2010-02-20	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID23-2	0.8726	ESRF	ID23-2

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	40	93.5	0.038	18.9	1.9	78348	73258		-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	1.8	1.86	77.6		0.25	2.73	1.6	6096

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	pdb entry 3UPL	1.8	39.55	73258	69601	3657	93.45	0.1648	0.1648	0.1627	0.2042	RANDOM	18.47

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]
0.86	-0.23	-0.37	-0.32	0.57	-0.63

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.97
r_dihedral_angle_4_deg	19.482
r_dihedral_angle_3_deg	13.69
r_dihedral_angle_1_deg	6.145
r_scangle_it	4.802
r_scbond_it	2.964
r_angle_refined_deg	1.835
r_mcangle_it	1.688
r_angle_other_deg	1.068
r_mcbond_it	1.002

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.97
r_dihedral_angle_4_deg	19.482
r_dihedral_angle_3_deg	13.69
r_dihedral_angle_1_deg	6.145
r_scangle_it	4.802
r_scbond_it	2.964
r_angle_refined_deg	1.835
r_mcangle_it	1.688
r_angle_other_deg	1.068
r_mcbond_it	1.002
r_mcbond_other	0.336
r_chiral_restr	0.116
r_bond_refined_d	0.023
r_gen_planes_refined	0.009
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6502
Nucleic Acid Atoms
Solvent Atoms	655
Heterogen Atoms	13

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
DNA	data collection
MOLREP	phasing

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.