2V5H | pdb_00002v5h

Controlling the storage of nitrogen as arginine: the complex of PII and acetylglutamate kinase 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	2JJ4	PDB ENTRY 2JJ4

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		8.5		0.1 M TRIS-HCL PH 8.5, 0.15 M SODIUM ACETATE, 20% (WT/VOL) POLYETHYLENE GLYCOL 4K, 20 MM ACETYLGLUTAMATE.

Crystal Properties
Matthews coefficient	Solvent content
2.3	45.1

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 90.379	α = 90
b = 161.027	β = 106.53
c = 91.562	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	ADSC CCD	RD COATED FLAT MIRROR AND RD COATED TOROIDAL MIRROR	2006-03-21	M	SINGLE WAVELENGTH
2	1	x-ray	100	CCD	MARRESEARCH			M

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID14-3		ESRF	ID14-3
2	SYNCHROTRON	ESRF BEAMLINE BM16		ESRF	BM16

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	2.75	87.71	100	0.08	6.9	5.1		65178		2	61.3

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	2.75	2.9	100		0.37	2	5.2

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 2JJ4	2.75	50	61827	3297	100	0.202	0.2	0.2	0.236	RANDOM	38.31

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]
-0.2		0.09	-0.25		0.5

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.972
r_dihedral_angle_4_deg	22.311
r_dihedral_angle_3_deg	18.875
r_dihedral_angle_1_deg	6.396
r_scangle_it	2.573
r_scbond_it	1.419
r_angle_refined_deg	1.375
r_mcangle_it	0.796
r_mcbond_it	0.394
r_symmetry_hbond_refined	0.389
r_nbtor_refined	0.313
r_symmetry_vdw_refined	0.237
r_nbd_refined	0.22
r_xyhbond_nbd_refined	0.148
r_chiral_restr	0.096
r_bond_refined_d	0.011
r_gen_planes_refined	0.004
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_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	17828
Nucleic Acid Atoms
Solvent Atoms	187
Heterogen Atoms	96

Software

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