2HMF

Structure of a Threonine Sensitive Aspartokinase from Methanococcus jannaschii Complexed with Mg-ADP and Aspartate

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2CDQ

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8.5	293	100 mM Tris pH 8.5 800 mM ammonium formate 13% PEG 3350, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.51	51.04

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 101.741	α = 90
b = 104.508	β = 90
c = 192.92	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	MAR CCD 165 mm		2003-12-16	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 14-ID-B	1	APS	14-ID-B

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	2.5	50	84.6	0.046	18.4		60800	60800	2	2

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)
	2.5	2.59	37		0.277			2612

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	Number Reflections (All)	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	2CDQ	2.7	50	2	60800	53864	2727	94.12	0.243	0.241	0.276	RANDOM	47.452

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]
-3.17			-0.96		4.14

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.037
r_dihedral_angle_3_deg	18.294
r_dihedral_angle_4_deg	17.236
r_dihedral_angle_1_deg	5.453
r_scangle_it	1.665
r_angle_refined_deg	1.222
r_scbond_it	0.948
r_mcangle_it	0.791
r_mcbond_it	0.472
r_nbtor_refined	0.303

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.037
r_dihedral_angle_3_deg	18.294
r_dihedral_angle_4_deg	17.236
r_dihedral_angle_1_deg	5.453
r_scangle_it	1.665
r_angle_refined_deg	1.222
r_scbond_it	0.948
r_mcangle_it	0.791
r_mcbond_it	0.472
r_nbtor_refined	0.303
r_symmetry_vdw_refined	0.294
r_symmetry_hbond_refined	0.261
r_nbd_refined	0.209
r_xyhbond_nbd_refined	0.133
r_chiral_restr	0.087
r_bond_refined_d	0.009
r_gen_planes_refined	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	14160
Nucleic Acid Atoms
Solvent Atoms	123
Heterogen Atoms	148

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
PHASER	phasing

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.