3B49

Crystal structure of an uncharacterized conserved protein from Listeria innocua

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	294	0.1M HEPES pH 7.5, 1.4M tri-Sodium citrate, VAPOR DIFFUSION, SITTING DROP, temperature 294K

Crystal Properties
Matthews coefficient	Solvent content
2.38	48.39

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 50.506	α = 90
b = 68.108	β = 90
c = 69.853	γ = 90

Symmetry
Space Group	P 21 21 21

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 315	Mirrors	2007-08-10	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 19-ID	0.97940	APS	19-ID

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	1.6	40	97.2	0.077	26.6	6	31607	31607

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	1.6	1.64	82.2		0.369	2.1

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		THROUGHOUT	1.6	30	31607	31539	1009	97.14	0.175	0.171	0.17	0.198	RANDOM	13.389

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]
-0.46			0.55		-0.09

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.296
r_dihedral_angle_4_deg	14.912
r_dihedral_angle_3_deg	11.407
r_dihedral_angle_1_deg	5.837
r_scangle_it	3.099
r_scbond_it	2.258
r_angle_refined_deg	1.318
r_mcangle_it	1.256
r_mcbond_it	1.13
r_angle_other_deg	0.802
r_symmetry_vdw_other	0.261
r_mcbond_other	0.225
r_nbd_refined	0.206
r_nbd_other	0.189
r_nbtor_refined	0.179
r_symmetry_hbond_refined	0.166
r_xyhbond_nbd_refined	0.145
r_symmetry_vdw_refined	0.143
r_nbtor_other	0.086
r_chiral_restr	0.078
r_bond_refined_d	0.012
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	1685
Nucleic Acid Atoms
Solvent Atoms	295
Heterogen Atoms	12

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
SBC-Collect	data collection
HKL-3000	data reduction
HKL-3000	data scaling
HKL2Map	phasing
SHELXCD	phasing
SHELXE	model building
SHELXD	phasing
ARP/wARP	model building