3OQ8 | pdb_00003oq8

Crystal structure of isocitrate lyase from Brucella melitensis, bound to the product mimic malonate

X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7	289	Internal tracking number 217291H3. Hampton INDEX Screen condition H3: 0.2 M sodium malonate pH 7.0, 20% PEG3350, BrabA.00014.a.A1 PW 25251 at 26 mg/mL, VAPOR DIFFUSION, SITTING DROP, temperature 289K

Crystal Properties
Matthews coefficient	Solvent content
2.54	51.58

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 77.5	α = 90
b = 136.03	β = 90
c = 181.77	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+		2010-08-22	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU FR-E SUPERBRIGHT	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	2.25	39.2	99.3	0.14	10.38	4.8	91893	91241		-3	24.311

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	2.25	2.31	99.2		0.479	4.2	4.6	6734

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	3EOL	2.25	39.2	91893	90916	4530	98.97	0.151	0.151	0.149	0.15	0.199	0.2	RANDOM	16.324

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]
0.56			0.47		-1.03

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.489
r_dihedral_angle_4_deg	18.468
r_dihedral_angle_3_deg	13.625
r_dihedral_angle_1_deg	6.013
r_scangle_it	3.426
r_scbond_it	2.145
r_angle_refined_deg	1.494
r_mcangle_it	1.108
r_angle_other_deg	0.951
r_mcbond_it	0.604

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.489
r_dihedral_angle_4_deg	18.468
r_dihedral_angle_3_deg	13.625
r_dihedral_angle_1_deg	6.013
r_scangle_it	3.426
r_scbond_it	2.145
r_angle_refined_deg	1.494
r_mcangle_it	1.108
r_angle_other_deg	0.951
r_mcbond_it	0.604
r_mcbond_other	0.204
r_chiral_restr	0.088
r_bond_refined_d	0.017
r_gen_planes_refined	0.007
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	12903
Nucleic Acid Atoms
Solvent Atoms	1177
Heterogen Atoms	81

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.