4EUV | pdb_00004euv

Crystal Structure of PelD 158-CT from Pseudomonas aeruginosa PAO1, in complex with c-di-GMP, form 1

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	hanging drop	6.5	298	50 mM sodium cacodylate, pH 6.5, 10 mM MgSO4, 1.3 M Li2SO4, hanging drop, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.23	44.85

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 59.531	α = 90
b = 41.516	β = 110.95
c = 64.402	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		IMAGE PLATE	MAR scanner 300 mm plate			M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 21-ID-F	1.0	APS	21-ID-F

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	50	99.1	0.09	8.2	6.8		19997

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	2.03	95.1		0.402		5.3	951

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	MOLECULAR REPLACEMENT	THROUGHOUT	2	25	19948	1022	98.98	0.2236	0.2205	0.24	0.2812	0.3	RANDOM	45.95

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]
-1.47		-2.22	0.15		-0.28

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.741
r_dihedral_angle_3_deg	18.307
r_dihedral_angle_4_deg	14.269
r_dihedral_angle_1_deg	6.116
r_scangle_it	3.132
r_scbond_it	2.013
r_angle_refined_deg	1.517
r_mcangle_it	1.28
r_mcbond_it	0.693
r_chiral_restr	0.092

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.741
r_dihedral_angle_3_deg	18.307
r_dihedral_angle_4_deg	14.269
r_dihedral_angle_1_deg	6.116
r_scangle_it	3.132
r_scbond_it	2.013
r_angle_refined_deg	1.517
r_mcangle_it	1.28
r_mcbond_it	0.693
r_chiral_restr	0.092
r_bond_refined_d	0.013
r_gen_planes_refined	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2256
Nucleic Acid Atoms
Solvent Atoms	128
Heterogen Atoms	46

Software

Software
Software Name	Purpose
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction

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.