3OCE

Crystal structure of fumarate lyase:delta crystallin from Brucella melitensis bound to cobalt

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1JSW	PDB entry 1jsw

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8.5	289	46.3 mg/mL BrabA.00047.a.A6 PS00513 against JCSG+ condition G3, 10 mM CoCl2, 0.1 M Tris, 20% polyvinyl pyrrolidone K15 with 20% ethylene glycol as cryo-protectant, crsytal tracking ID 215219g3, 3C protease cleaved, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 289K

Crystal Properties
Matthews coefficient	Solvent content
3.14	60.87

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 95.33	α = 90
b = 113.55	β = 90
c = 236.86	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	ADSC QUANTUM 315r		2010-06-25	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 5.0.2	1.0	ALS	5.0.2

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	2.58	50	99.1	0.146	10.03	7.1	81644	80944		-3	29.903

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)
	2.58	2.65	99		0.565	3.1

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	PDB entry 1jsw	2.58	50	80691	4054	98.85	0.1984	0.1959	0.2454	RANDOM	29.6871

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]
-1.65			-0.06		1.71

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.22
r_dihedral_angle_3_deg	18.128
r_dihedral_angle_4_deg	17.4
r_dihedral_angle_1_deg	5.793
r_scangle_it	3.558
r_scbond_it	1.999
r_angle_refined_deg	1.538
r_mcangle_it	1.227
r_mcbond_it	0.624
r_chiral_restr	0.104

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.22
r_dihedral_angle_3_deg	18.128
r_dihedral_angle_4_deg	17.4
r_dihedral_angle_1_deg	5.793
r_scangle_it	3.558
r_scbond_it	1.999
r_angle_refined_deg	1.538
r_mcangle_it	1.227
r_mcbond_it	0.624
r_chiral_restr	0.104
r_bond_refined_d	0.014
r_gen_planes_refined	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	13775
Nucleic Acid Atoms
Solvent Atoms	544
Heterogen Atoms	20

Software

Software
Software Name	Purpose
XSCALE	data scaling
MOLREP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
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.