3UPL | pdb_00003upl

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

X-RAY DIFFRACTION

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, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.28	45.94

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 49.365	α = 68.63
b = 63.38	β = 75.8
c = 79.123	γ = 72.7

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	1.5	40	96.8	0.044	28.8	2.9	134090	129797		-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	1.5	1.55	92.5		0.2	4.7	2.4	12350

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 (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	SAD	THROUGHOUT	1.5	25	129797	123302	6476	94.9	0.1514	0.1514	0.15	0.16	0.1763	0.18	RANDOM	13.276

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]
0.26	-0.17	-0.28	0.06	0.31	-0.3

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.091
r_dihedral_angle_4_deg	21.183
r_dihedral_angle_3_deg	12.193
r_dihedral_angle_1_deg	8.4
r_scangle_it	4.941
r_scbond_it	2.997
r_angle_refined_deg	1.964
r_mcangle_it	1.79
r_mcbond_it	1.083
r_angle_other_deg	1.077

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.091
r_dihedral_angle_4_deg	21.183
r_dihedral_angle_3_deg	12.193
r_dihedral_angle_1_deg	8.4
r_scangle_it	4.941
r_scbond_it	2.997
r_angle_refined_deg	1.964
r_mcangle_it	1.79
r_mcbond_it	1.083
r_angle_other_deg	1.077
r_mcbond_other	0.356
r_chiral_restr	0.123
r_bond_refined_d	0.022
r_gen_planes_refined	0.01
r_bond_other_d	0.002
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6516
Nucleic Acid Atoms
Solvent Atoms	852
Heterogen Atoms	20

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
SHELX	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
DNA	data collection
DMMulti	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.