4KMQ | pdb_00004kmq

1.9 Angstrom resolution crystal structure of uncharacterized protein lmo2446 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	8.3	295	crystallization conditions - The JCSG+ suite (A5: 200 mM Magnesium formate, 20 % w/v PEG3350), protein - 7.1 mg/mL in 10 mM Tris/HCl pH8.3, 500 mM NaCl, 5 mM BME, cryo - soaked in crystallization condition solution, VAPOR DIFFUSION, SITTING DROP, temperature 295K

Crystal Properties
Matthews coefficient	Solvent content
2.47	50.28

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 164.858	α = 90
b = 102.359	β = 104.86
c = 74.334	γ = 90

Symmetry
Space Group	C 1 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 225 mm CCD	BE-LENSES/DIAMOND LAUE MONO	2013-03-15	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 21-ID-F	0.97872	APS	21-ID-F

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	1.9	30	99.7	0.067	22.1	2.5		185978		-3	28.4

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	1.9	1.93	100		0.502	2	2.6	9248

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 (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	1.9	29.66	88907	88907	4702	99.78	0.15269	0.15103	0.1524	0.18352	0.1832	RANDOM	30.733

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]
1.17		0.39	-1.61		0.64

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.241
r_dihedral_angle_4_deg	12.918
r_dihedral_angle_3_deg	9.28
r_scangle_it	3.636
r_dihedral_angle_1_deg	3.266
r_scbond_it	2.387
r_angle_refined_deg	1.591
r_mcangle_it	1.312
r_angle_other_deg	0.84
r_mcbond_it	0.752
r_mcbond_other	0.244
r_chiral_restr	0.102
r_bond_refined_d	0.013
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	8327
Nucleic Acid Atoms
Solvent Atoms	1013
Heterogen Atoms	8

Software

Software
Software Name	Purpose
Blu-Ice	data collection
MLPHARE	phasing
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling