3BLC

Crystal structure of the periplasmic domain of the Escherichia Coli YIDC

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	3.1	295	0.1 M glycine, 0.2 M ammonium sulfate, 13% PEG3350, pH 3.1, VAPOR DIFFUSION, HANGING DROP, temperature 295K

Crystal Properties
Matthews coefficient	Solvent content
3.99	69.15

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 126.127	α = 90
b = 126.127	β = 90
c = 288.459	γ = 90

Symmetry
Space Group	I 41 2 2

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	2007-08-02	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 8.2.2	0.9794	ALS	8.2.2

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	2.5	50	99.1	0.079	0.079	44.7	13.8		40327	2	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	2.5	2.6	92		0.379	0.379	4	9.7	3687

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	SAD	THROUGHOUT	2.5	50	38278	2021	98.93	0.2135	0.21165	0.24897	RANDOM	34.447

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]
2.13			2.13		-4.26

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.488
r_dihedral_angle_3_deg	18.498
r_dihedral_angle_4_deg	17.166
r_dihedral_angle_1_deg	6.994
r_scangle_it	2.62
r_scbond_it	1.819
r_angle_refined_deg	1.515
r_mcangle_it	1.018
r_mcbond_it	0.665
r_nbtor_refined	0.315
r_symmetry_vdw_refined	0.227
r_nbd_refined	0.223
r_symmetry_hbond_refined	0.174
r_xyhbond_nbd_refined	0.142
r_chiral_restr	0.103
r_bond_refined_d	0.015
r_gen_planes_refined	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4291
Nucleic Acid Atoms
Solvent Atoms	80
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
ADSC	data collection
HKL-2000	data reduction
HKL-2000	data scaling
SHELXS	phasing