3ZZG | pdb_00003zzg

Crystal structure of the amino acid kinase domain from Saccharomyces cerevisiae acetylglutamate kinase without ligands

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3ZZF	PDB ENTRY 3ZZF

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		4.6		PROTEIN WAS CRYSTALLIZED IN 50 MM NA-ACETATE, PH 4.6, 0.2 M NA-MALONATE AND 2% PEG 8000,, CONTAINING 24MM N-ACETYLGLUTAMATE (NAG); PREVIOUS TO FREEZING, CRYSTAL WAS WASHED 6 HOURS IN CRYSTALLIZATION BUFFER WITHOUT NAG. 25% GLYCEROL WAS USED AS CRYOPROTECTOR

Crystal Properties
Matthews coefficient	Solvent content
2.38	48

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 68.086	α = 90
b = 100.531	β = 90
c = 188.74	γ = 90

Symmetry
Space Group	P 21 21 21

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		2011-03-03	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID14-4		ESRF	ID14-4

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	2.95	20	99.8	0.07	8.3	6.4		28023		2.1	79.7

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	2.95	3.11	99.8		0.37	2.1	6.5

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 (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 3ZZF	2.95	20	26458	1398	99.75	0.21357	0.21189	0.21	0.24521	0.24	RANDOM	81.447

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]
2.3			-4.04		1.74

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.021
r_dihedral_angle_3_deg	17.202
r_dihedral_angle_4_deg	16.96
r_dihedral_angle_1_deg	5.749
r_scangle_it	1.585
r_angle_refined_deg	1.078
r_scbond_it	0.884
r_angle_other_deg	0.821
r_mcangle_it	0.774
r_mcbond_it	0.408
r_chiral_restr	0.062
r_mcbond_other	0.051
r_bond_refined_d	0.009
r_gen_planes_refined	0.003
r_bond_other_d	0.002
r_gen_planes_other	0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
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	8978
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
SCALA	data scaling
PHASER	phasing