3RQI

Crystal structure of a response regulator protein from Burkholderia pseudomallei with a phosphorylated aspartic acid, calcium ion and citrate

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	4.2	289	BupsA.00608.a.A1 PW30798 at 30.69 mg/mL against JCSG+ screen condition A6, 0.2 M Li2SO4, 0.1 M phosphate/citrate pH 4.2, 20% PEG 1000 with 25% ethylene glycol as cryo-protectant, crystal tracking ID 220922a6, VAPOR DIFFUSION, SITTING DROP, temperature 289K

Crystal Properties
Matthews coefficient	Solvent content
2.08	40.97

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 55.24	α = 90
b = 55.24	β = 90
c = 95.42	γ = 120

Symmetry
Space Group	P 31 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	ADSC QUANTUM 315r		2011-04-10	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 5.0.1	0.97740	ALS	5.0.1

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	1.7	50	99.5	0.049	23.22	6.2	19149	19044		-3	25.389

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)
	1.7	1.74	99.8		0.509	3.76	5.1	1393

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	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	MOLECULAR REPLACEMENT	THROUGHOUT	1zy2	1.7	50	19018	976	99.12	0.2081	0.2064	0.2395	RANDOM	24.9592

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]
-0.81	-0.41		-0.81		1.22

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.372
r_dihedral_angle_4_deg	13.979
r_dihedral_angle_3_deg	12.393
r_dihedral_angle_1_deg	5.133
r_scangle_it	3.921
r_scbond_it	2.415
r_angle_refined_deg	1.486
r_mcangle_it	1.399
r_mcbond_it	0.794
r_chiral_restr	0.102

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.372
r_dihedral_angle_4_deg	13.979
r_dihedral_angle_3_deg	12.393
r_dihedral_angle_1_deg	5.133
r_scangle_it	3.921
r_scbond_it	2.415
r_angle_refined_deg	1.486
r_mcangle_it	1.399
r_mcbond_it	0.794
r_chiral_restr	0.102
r_bond_refined_d	0.015
r_gen_planes_refined	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1261
Nucleic Acid Atoms
Solvent Atoms	127
Heterogen Atoms	30

Software

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

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM133198.