4K15 | pdb_00004k15

2.75 Angstrom Crystal Structure of Hypothetical Protein lmo2686 from Listeria monocytogenes EGD-e

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5.5	295	7.2 mg/mL protein in 0.5 M sodium chloride, 0.1 M Tris-HCl, pH 8.3 against Classics II screen (A9): 0.1 M Bis-Tris, pH 5.5, 3 M sodium chloride, cryoprotectant: paratone, VAPOR DIFFUSION, SITTING DROP, temperature 295K

Crystal Properties
Matthews coefficient	Solvent content
2.43	49.39

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 91.093	α = 90
b = 91.093	β = 90
c = 125.47	γ = 120

Symmetry
Space Group	P 32 2 1

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	mirrors	2013-03-28	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 21-ID-G	0.97911	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	2.75	30	99.8	0.077	23.6	4.4	16172	16172		-3	79.3

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	2.75	2.8	100		0.565	2.7	4.5	787

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	SAD	THROUGHOUT	2.75	29.82	15304	15304	804	99.77	0.19836	0.19836	0.19629	0.1969	0.24024	0.2384	RANDOM	59.308

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]
2.78	1.39		2.78		-4.17

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	29.396
r_dihedral_angle_3_deg	8.091
r_dihedral_angle_4_deg	4.822
r_scangle_it	2.988
r_dihedral_angle_1_deg	2.249
r_scbond_it	1.826
r_angle_refined_deg	1.458
r_mcangle_it	1.218
r_angle_other_deg	0.708
r_mcbond_it	0.627
r_mcbond_other	0.1
r_chiral_restr	0.075
r_bond_refined_d	0.008
r_gen_planes_refined	0.004
r_bond_other_d	0.001
r_gen_planes_other

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3095
Nucleic Acid Atoms
Solvent Atoms	98
Heterogen Atoms	2

Software

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