4LYK | pdb_00004lyk

Crystal structure of the EAL domain of c-di-GMP specific phosphodiesterase YahA in complex with activating cofactor Mg++

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4KIE

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.5	293	12.5% w/v PEG 1000, 12.5% w/v PEG 3350, 12.5% v/v MPD, 10 % of amino acid mixture (200 mM of each of Sodium-L-glutamate, M DL-alanine, Glycin and L-Lysine HCl, 0.2 M DL-Serin), 100 mM MES/Imidazole pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.31	46.74

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 64.85	α = 90
b = 109.547	β = 99.39
c = 81.75	γ = 90

Symmetry
Space Group	P 1 21 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	PIXEL	DECTRIS PILATUS 2M		2012-09-03	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X06DA	1.0000	SLS	X06DA

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	2.4	109.55	99.63	0.053	14.5822	3.4		43912		-3

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	2.4	2.53	99.79		0.45	1.76	3.31	6344

Refinement

Statistics
Diffraction ID	Structure Solution Method	Starting model	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)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	4KIE	2.4	30	43884	2209	99.58	0.1902	0.1886	0.19	0.222	0.22	50.282

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]
-1.95		-1.56	-0.18		2.26

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.807
r_dihedral_angle_4_deg	18.817
r_dihedral_angle_3_deg	17.533
r_dihedral_angle_1_deg	5.403
r_angle_refined_deg	1.423
r_angle_other_deg	1.192
r_chiral_restr	0.081
r_bond_refined_d	0.013
r_gen_planes_refined	0.008
r_bond_other_d	0.007

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.807
r_dihedral_angle_4_deg	18.817
r_dihedral_angle_3_deg	17.533
r_dihedral_angle_1_deg	5.403
r_angle_refined_deg	1.423
r_angle_other_deg	1.192
r_chiral_restr	0.081
r_bond_refined_d	0.013
r_gen_planes_refined	0.008
r_bond_other_d	0.007
r_gen_planes_other	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	7881
Nucleic Acid Atoms
Solvent Atoms	233
Heterogen Atoms	60

Software

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

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), 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 R01GM157729.