7CMY

Isocitrate lyase from Bacillus cereus ATCC 14579 in complex with Magnessium ion, glyoxylate, and succinate

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293	50% PEG 400, 100mM CHES pH 9.5, 200mM NaCl

Crystal Properties
Matthews coefficient	Solvent content
2.3	46.56

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 94.91	α = 90
b = 94.91	β = 90
c = 196.156	γ = 90

Symmetry
Space Group	P 41 21 2

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 270		2020-07-16	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PAL/PLS BEAMLINE 7A (6B, 6C1)	0.97934	PAL/PLS	7A (6B, 6C1)

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	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	2.5	50	98.3	0.178	0.199	0.086	7.7	5.3		31543

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.5	2.54	99.3		1.201	1.33	0.556	0.625		5.5

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	3I4E	2.5	36.28	29820	1563	98.01	0.2007	0.1964	0.2831	RANDOM	45.827

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]
-0.25			-0.25		0.51

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.969
r_dihedral_angle_4_deg	19.771
r_dihedral_angle_3_deg	16.586
r_dihedral_angle_1_deg	7.52
r_angle_refined_deg	1.672
r_angle_other_deg	1.329
r_chiral_restr	0.077
r_bond_refined_d	0.009
r_gen_planes_refined	0.007
r_bond_other_d	0.001

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.969
r_dihedral_angle_4_deg	19.771
r_dihedral_angle_3_deg	16.586
r_dihedral_angle_1_deg	7.52
r_angle_refined_deg	1.672
r_angle_other_deg	1.329
r_chiral_restr	0.077
r_bond_refined_d	0.009
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	6454
Nucleic Acid Atoms
Solvent Atoms	193
Heterogen Atoms	28

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-2000	data scaling
PDB_EXTRACT	data extraction
HKL-2000	data reduction
MOLREP	phasing

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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.