3DFE | pdb_00003dfe

Crystal structure of a Putative Pii-Like Signaling Protein (YP_323533.1) from ANABAENA VARIABILIS ATCC 29413 at 2.35 A resolution

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5.5	293	35.0000% 2-propanol, 5.0000% PEG-1000, 35.0000% 2-propanol, 5.0000% PEG-1000, 0.1M Citrate pH 5.5, NANODROP', VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.21	44.32

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 63.491	α = 90
b = 78.749	β = 100.56
c = 65.544	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	CCD	MARMOSAIC 325 mm CCD	Flat mirror (vertical focusing)	2008-04-03	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL11-1	0.91837,0.97854	SSRL	BL11-1

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	2.35	29.814	99.9	0.059	0.059	7.9	3.8		26560			57.051

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	2.35	2.41	100		0.606	0.606	1.3	3.8	1948

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	MAD	THROUGHOUT	2.35	29.814	26543	1339	99.93	0.227	0.224	0.23	0.267	0.27	RANDOM	48.862

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]
4.43		4.08	-1.25		-1.68

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.407
r_dihedral_angle_4_deg	17.273
r_dihedral_angle_3_deg	12.554
r_dihedral_angle_1_deg	3.294
r_angle_refined_deg	1.621
r_scangle_it	1.248
r_mcangle_it	1.089
r_angle_other_deg	0.997
r_scbond_it	0.981
r_mcbond_it	0.734
r_mcbond_other	0.323
r_symmetry_vdw_refined	0.277
r_nbd_refined	0.203
r_nbd_other	0.184
r_nbtor_refined	0.18
r_symmetry_vdw_other	0.161
r_xyhbond_nbd_refined	0.127
r_chiral_restr	0.099
r_nbtor_other	0.087
r_bond_refined_d	0.015
r_bond_other_d	0.006
r_gen_planes_refined	0.005
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3582
Nucleic Acid Atoms
Solvent Atoms	21
Heterogen Atoms	8

Software

Software
Software Name	Purpose
REFMAC	refinement
PHENIX	refinement
SHELX	phasing
MolProbity	model building
SCALA	data scaling
PDB_EXTRACT	data extraction
MOSFLM	data reduction
autoSHARP	phasing