2XG8

Structural basis of gene regulation by protein PII: The crystal complex of PII and PipX from Synechococcus elongatus PCC 7942

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1V5H	PDB ENTRY 1V5H, CHAIN J

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		7.5		PII-PIPX COMPLEX AT 5.5 MG/ML IN 20 MM HEPES PH 7.5, 1MM DTT, 0.4 M NACL, 5 MM MAGNESIUM CHLORIDE. PRECIPITANT SOLUTION: 15 % PEG 3.35K, 0.2 M SODIUM FORMATE.

Crystal Properties
Matthews coefficient	Solvent content
2.19	43.82

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 111.383	α = 90
b = 61.585	β = 126.44
c = 112.979	γ = 90

Symmetry
Space Group	C 1 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 CCD		2007-11-10	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID29		ESRF	ID29

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	3.2	90.9	99.9	0.11	7.1	3.9		10330		1.8	74.4

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	3	3.37	99.9		0.42	1.8	3.9

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	PDB ENTRY 1V5H, CHAIN J	3.2	50	9829	495	99.83	0.22923	0.22708	0.27247	RANDOM	70.104

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]
1.51		1.6	0.05		0.35

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.799
r_dihedral_angle_3_deg	17.696
r_dihedral_angle_4_deg	14.408
r_dihedral_angle_1_deg	8.25
r_angle_refined_deg	1.259
r_angle_other_deg	1.009
r_scangle_it	0.763
r_scbond_it	0.475
r_mcangle_it	0.375
r_mcbond_it	0.337
r_symmetry_hbond_refined	0.3
r_symmetry_vdw_refined	0.244
r_symmetry_vdw_other	0.236
r_nbd_refined	0.228
r_nbd_other	0.192
r_nbtor_refined	0.181
r_chiral_restr	0.142
r_xyhbond_nbd_refined	0.122
r_nbtor_other	0.083
r_mcbond_other	0.031
r_bond_refined_d	0.008
r_bond_other_d	0.003
r_gen_planes_refined	0.003
r_gen_planes_other	0.002
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4529
Nucleic Acid Atoms
Solvent Atoms	3
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
MOLREP	phasing