3WZ4 | pdb_00003wz4

Structure of the periplasmic domain of DotI (crystal form I)

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	10.5	277	0.1M CAPS pH10.5, 40% MPD, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
3.49	64.8

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 145.59	α = 90
b = 207.577	β = 90
c = 58.179	γ = 90

Symmetry
Space Group	P 21 21 2

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	35	CCD	RAYONIX MX225HE		2010-11-01	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SPRING-8 BEAMLINE BL41XU	0.97923	SPring-8	BL41XU

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	54	98.4	0.127	0.127	9.3	5.8	88995	88995			20.2

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	2.2	2.32	94.6		0.321	4	4.5	12299

Refinement

Statistics
Diffraction ID	Structure Solution Method	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	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	2.2	37.425	1.34	88906	2000	98.21	0.1918	0.1908	0.1907	0.2353	0.2309	RANDOM

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]
0.5948			-3.0756		2.4808

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	17.323
f_angle_d	0.635
f_chiral_restr	0.045
f_bond_d	0.003
f_plane_restr	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	8514
Nucleic Acid Atoms
Solvent Atoms	1256
Heterogen Atoms	256

Software

Software
Software Name	Purpose
SPring-8	data collection
PHENIX	model building
PHENIX	refinement
MOSFLM	data reduction
SCALA	data scaling
PHENIX	phasing