4IIW

2.6 Angstrom Crystal Structure of Putative yceG-like Protein lmo1499 from Listeria monocytogenes

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.5	295	Protein: 7.1mg/mL, 0.25M Sodium cloride, 0.01M Tris-HCl pH 8.3, Screen: Trap96 (E8), 0.2M Ammonium sulfate, 0.1M Cacodyl. pH 6.5, 30% (w/v) PEG 8000, VAPOR DIFFUSION, SITTING DROP, temperature 295K

Crystal Properties
Matthews coefficient	Solvent content
2.91	57.77

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 126.899	α = 90
b = 126.899	β = 90
c = 115.584	γ = 90

Symmetry
Space Group	I 4

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	MARMOSAIC 300 mm CCD	Beryllium lenses	2012-12-10	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 21-ID-G	0.97856	APS	21-ID-G

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	2.6	30	99.6	0.063	26.1	3.9	55066	55066		-3	69.9

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	2.6	2.64	100		0.567	2.4	3.9	2698

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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	SAD	THROUGHOUT	2.6	29.91	26680	26680	1414	99.87	0.17317	0.17317	0.17096	0.215	RANDOM	54.203

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]
-0.17			-0.17		0.34

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.549
r_dihedral_angle_4_deg	19.279
r_dihedral_angle_3_deg	11.109
r_scangle_it	4.566
r_scbond_it	2.969
r_dihedral_angle_1_deg	2.575
r_mcangle_it	1.833
r_angle_refined_deg	1.304
r_mcbond_it	0.974
r_angle_other_deg	0.794

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.549
r_dihedral_angle_4_deg	19.279
r_dihedral_angle_3_deg	11.109
r_scangle_it	4.566
r_scbond_it	2.969
r_dihedral_angle_1_deg	2.575
r_mcangle_it	1.833
r_angle_refined_deg	1.304
r_mcbond_it	0.974
r_angle_other_deg	0.794
r_mcbond_other	0.232
r_chiral_restr	0.078
r_bond_refined_d	0.011
r_gen_planes_refined	0.005
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4836
Nucleic Acid Atoms
Solvent Atoms	188
Heterogen Atoms	46

Software

Software
Software Name	Purpose
Blu-Ice	data collection
PHENIX	model building
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling
PHENIX	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.