4MCW | pdb_00004mcw

Crystal structure of a HD-GYP domain (a cyclic-di-GMP phosphodiesterase) containing a tri-nuclear metal centre

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6	277	0.9 M succinate pH 7, 2% PEG 2000, 0.1 M MES pH 6 , VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
4.36	71.81

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 69.83	α = 90
b = 182.38	β = 90
c = 232.47	γ = 90

Symmetry
Space Group	I 2 2 2

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	PSI PILATUS 6M	mirrors	2013-03-22	M	SINGLE WAVELENGTH
2	1

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I02	2.03	Diamond	I02
2				Diamond	I24

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	2.03	71.75	99.4	0.041	0.041	15.6	4	101947	95399		-3	52.8

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.03	2.1	98		0.56	0.56	2.3	4

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (All)	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	2.03	71.75	91103	90598	4783	99.4	0.18863	0.18732	0.18	0.21278	0.21	RANDOM	52.854

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]
-1.09			2.24		-1.15

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.826
r_dihedral_angle_3_deg	15.569
r_dihedral_angle_4_deg	15.308
r_dihedral_angle_1_deg	5.394
r_angle_refined_deg	1.363
r_chiral_restr	0.091
r_bond_refined_d	0.011
r_gen_planes_refined	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5929
Nucleic Acid Atoms
Solvent Atoms	404
Heterogen Atoms	63

Software

Software
Software Name	Purpose
EDNA	data collection
SHELX	model building
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
SHELX	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.