3IB6 | pdb_00003ib6

Crystal structure of an uncharacterized protein from Listeria monocytogenes serotype 4b

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	7	294	16% PEG 3350, 100mM ammonium chloride, pH 7.0, vapor diffusion, temperature 294K

Crystal Properties
Matthews coefficient	Solvent content
2.15	42.81

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 41.122	α = 90
b = 125.97	β = 103.58
c = 73.385	γ = 90

Symmetry
Space Group	P 1 21 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		2009-07-13	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 31-ID	0.97958	APS	31-ID

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym 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	2.2	38.101	99.8	0.115	0.115	6.3	4.2	36871	36797			41.2

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.2	2.32	100		0.463	0.463	2.1	4.2	5370

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	2.2	20	36780	36729	1849	99.86	0.221	0.218	0.2216	0.282	0.2799	RANDOM	52.616

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]
0.3		0.29	-1.11		0.95

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.881
r_dihedral_angle_4_deg	20.05
r_dihedral_angle_3_deg	16.587
r_dihedral_angle_1_deg	6.516
r_scangle_it	3.262
r_scbond_it	2.042
r_angle_refined_deg	1.529
r_mcangle_it	1.37
r_angle_other_deg	0.954
r_mcbond_it	0.745
r_mcbond_other	0.158
r_chiral_restr	0.088
r_bond_refined_d	0.015
r_gen_planes_refined	0.006
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5595
Nucleic Acid Atoms
Solvent Atoms	119
Heterogen Atoms

Software

Software
Software Name	Purpose
SCALA	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
MAR345	data collection
MOSFLM	data reduction
SHELXCD	phasing
SHELXE	model building