3P0X

Crystal structure of isocitrate lyase from Brucella melitensis, bound to magnesium isocitrate

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3OQ8

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6	290	Internal tracking number 217292B10. Protein (26 mg/mL) and PACT Screen condition B10: 0.2 M MgCl2, 20% PEG6000, 0.1 M MES pH 6.0, 5 mM isocitrate, VAPOR DIFFUSION, SITTING DROP, temperature 290K

Crystal Properties
Matthews coefficient	Solvent content
2.52	51.18

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 76.91	α = 90
b = 135.93	β = 90
c = 181.79	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	CCD	RIGAKU SATURN 944+		2010-08-26	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU MICROMAX-007 HF	1.541780

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	2.35	47.6	99.8	0.101	12.13	3.8	80134	79958		-3	28.906

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	2.35	2.41	99.2		0.563	2	2.9	5866

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	3OQ8	2.35	47.6	80134	79682	3991	99.46	0.18	0.18	0.178	0.23	RANDOM	22.264

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]
1.12			-0.38		-0.74

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.778
r_dihedral_angle_4_deg	17.585
r_dihedral_angle_3_deg	14.061
r_dihedral_angle_1_deg	5.671
r_scangle_it	2.34
r_scbond_it	1.417
r_angle_refined_deg	1.246
r_angle_other_deg	0.879
r_mcangle_it	0.818
r_mcbond_it	0.431

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.778
r_dihedral_angle_4_deg	17.585
r_dihedral_angle_3_deg	14.061
r_dihedral_angle_1_deg	5.671
r_scangle_it	2.34
r_scbond_it	1.417
r_angle_refined_deg	1.246
r_angle_other_deg	0.879
r_mcangle_it	0.818
r_mcbond_it	0.431
r_mcbond_other	0.113
r_chiral_restr	0.071
r_bond_refined_d	0.011
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	12879
Nucleic Acid Atoms
Solvent Atoms	687
Heterogen Atoms	80

Software

Software
Software Name	Purpose
XSCALE	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
StructureStudio	data collection
XDS	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.