3LR0 | pdb_00003lr0

Periplasmic domain of the risS sensor protein from Burkholderia pseudomallei, iodide phased at low pH

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	4.2	289	Crystal originally grown in JCSG+ condition a6, 0.1M phosphate-citrate pH 4.2, 0.2 M lithium sulfate, 25% PEG 1000 then soaked and cryo-protected into 0.1 M Na citrate pH 4.5, 1.0 M KI, 30% PEG 1000 for 1 hour prior to vitrification; crystal tracking IDs 203087a6 for growth and 206239a1 for soak; affinity tag not removed prior to crystallization, VAPOR DIFFUSION, SITTING DROP, temperature 289K

Crystal Properties
Matthews coefficient	Solvent content
2.26	45.64

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 58.36	α = 90
b = 58.36	β = 90
c = 75.69	γ = 120

Symmetry
Space Group	P 32 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	RIGAKU SATURN 944		2009-12-10	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU MICROMAX-007 HF	1.5418

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	19.1	99.8	0.046	25.45	11.2	12212	12191		-3	32.657

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	1.95	99.9		0.337	4.1	8.9	925

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	SAD	THROUGHOUT	1.9	19.1	12191	585	99.84	0.213	0.211	0.2142	0.254	0.2559	RANDOM	18.791

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	0.23		0.46		-0.69

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.792
r_dihedral_angle_4_deg	20.377
r_dihedral_angle_3_deg	14.385
r_dihedral_angle_1_deg	5.971
r_scangle_it	4.041
r_scbond_it	2.416
r_mcangle_it	1.568
r_angle_refined_deg	1.388
r_mcbond_it	0.864
r_chiral_restr	0.089
r_bond_refined_d	0.016
r_gen_planes_refined	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	806
Nucleic Acid Atoms
Solvent Atoms	71
Heterogen Atoms	6

Software

Software
Software Name	Purpose
XSCALE	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction