1UJQ

Crystal structure of 2-methylisocitrate lyase (PrpB) from Salmonella enterica serovar typhimurium

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.5	291	Imidazole,Sodium acetate trihydrate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K
2	VAPOR DIFFUSION, HANGING DROP	8	291	Sodium formate, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K
3	VAPOR DIFFUSION, SITTING DROP	8	291	Sodium chloride, PEG6000, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 291K
4	VAPOR DIFFUSION, SITTING DROP	4.5	277	Sodium formate, Sodium acetate trihydrate, pH 4.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 62.812	α = 90
b = 99.086	β = 90
c = 201.571	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	IMAGE PLATE	MARRESEARCH	Osmic mirrors	2003-02-05	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU RU200	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	100	92.9	0.061	0.061	15.5	5.5	74393	69022			27.7

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)
	2.1	2.17	97		0.421	0.423	5.2	5.8	7079

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	1MUM	2.1	19.99	69022	3514	92.9	0.205	0.205	0.232	RANDOM	38.8

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]
-5.42			6.09		-0.68

RMS Deviations
Key	Refinement Restraint Deviation
c_dihedral_angle_d	21.4
c_scangle_it	3.16
c_mcangle_it	2.23
c_scbond_it	2.17
c_mcbond_it	1.44
c_angle_deg	1.1
c_improper_angle_d	0.86
c_bond_d	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	8220
Nucleic Acid Atoms
Solvent Atoms	565
Heterogen Atoms

Software

Software
Software Name	Purpose
CNS	refinement
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	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 R01GM133198.