3ZZF | pdb_00003zzf

Crystal structure of the amino acid kinase domain from Saccharomyces cerevisiae acetylglutamate kinase complexed with its substrate N- acetylglutamate

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	Other		STARTING MODEL WAS A LOW RESOLUTION INCOMPLETE MODEL FROM A SE-MET SUBSTITUTED CRYSTAL

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; PREVIOUS TO FREEZING, CRYSTAL WAS SOAKED IN 2 MM HGCL2 AND 25% GLYCEROL AS CRYOPROTECTOR

Crystal Properties
Matthews coefficient	Solvent content
2.43	49

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 69.701	α = 90
b = 99.299	β = 90
c = 190.644	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		2009-07-25	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	2.2	19.97	100	0.12	5	15		67865		1.9	26.7

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	2.2	2.32	100		0.4	1.9	15.3

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	STARTING MODEL WAS A LOW RESOLUTION INCOMPLETE MODEL FROM A SE-MET SUBSTITUTED CRYSTAL	2.2	20	64245	3432	99.92	0.1807	0.1787	0.2	0.21812	0.23	RANDOM	26.165

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]
0.05			0.06		-0.11

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.377
r_dihedral_angle_3_deg	14.669
r_dihedral_angle_4_deg	14.062
r_dihedral_angle_1_deg	5.65
r_scangle_it	1.966
r_scbond_it	1.152
r_angle_refined_deg	1.038
r_angle_other_deg	0.804
r_mcangle_it	0.681
r_mcbond_it	0.343
r_mcbond_other	0.07
r_chiral_restr	0.059
r_bond_refined_d	0.008
r_gen_planes_refined	0.003
r_bond_other_d	0.001
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	8984
Nucleic Acid Atoms
Solvent Atoms	430
Heterogen Atoms	143

Software

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