2RD5 | pdb_00002rd5

Structural basis for the regulation of N-acetylglutamate kinase by PII in Arabidopsis thaliana

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2BUF	pdb entries 2BUF, 2O66
experimental model	PDB	2O66	pdb entries 2BUF, 2O66

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7	298	8.5% PEG 8000, 8.5% PEG 1000, 0.1 M Na-HEPES, 0.4 M TMAO, 50 mM L-aginine, 2 mM DTT, 12% (w/v) glycerol, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
4.54	72.89

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 171.133	α = 90
b = 171.133	β = 90
c = 171.133	γ = 90

Symmetry
Space Group	P 21 3

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 225 mm CCD	vertically focusing mirror	2007-03-24	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	CLSI BEAMLINE 08ID-1	1.3361	CLSI	08ID-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	2.5	40	100	0.127	0.127	38	17.7	57349	57349	-3	-3	61.9

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	2.5	2.59	100		0.95	0.95	3.2	14.8	5692

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	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	pdb entries 2BUF, 2O66	2.51	40	54380	54380	2907	99.93	0.20261	0.20261	0.20116	0.2	0.22928	0.22	RANDOM	67.497

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]

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.955
r_dihedral_angle_4_deg	16.713
r_dihedral_angle_3_deg	16.505
r_scangle_it	5.759
r_dihedral_angle_1_deg	5.441
r_scbond_it	4.2
r_mcangle_it	2.668
r_mcbond_it	1.802
r_angle_refined_deg	1.291
r_nbtor_refined	0.295
r_nbd_refined	0.19
r_symmetry_hbond_refined	0.185
r_symmetry_vdw_refined	0.158
r_xyhbond_nbd_refined	0.108
r_chiral_restr	0.08
r_bond_refined_d	0.008
r_gen_planes_refined	0.003
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_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6095
Nucleic Acid Atoms
Solvent Atoms	64
Heterogen Atoms	169

Software

Software
Software Name	Purpose
REFMAC	refinement
MxDC	data collection
HKL-2000	data reduction
SCALEPACK	data scaling
PHASER	phasing