1TJ7 | pdb_00001tj7

Structure determination and refinement at 2.44 A resolution of Argininosuccinate lyase from E. coli

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1K7W	PDB entry 1K7W

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7	294	Ammonium phosphate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 294K

Crystal Properties
Matthews coefficient	Solvent content
3.14	60.5

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 121.469	α = 90
b = 121.469	β = 90
c = 255.251	γ = 120

Symmetry
Space Group	P 61 2 2

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	MARRESEARCH	Bent mirror	2002-09-20	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	MAX II BEAMLINE I711	1.134	MAX II	I711

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	2.44	35	99.8	0.099	0.074	20.7	14.37		42164			35.43

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	2.44	2.53	98.7		0.401	0.437	6.06		4091

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 entry 1K7W	2.44	20	39912	39912	2021	99.81	0.1694	0.16942	0.16689	0.21	0.21742	0.25	RANDOM	19.764

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_1_deg	5.603
r_scangle_it	3.515
r_scbond_it	2.17
r_angle_refined_deg	1.537
r_mcangle_it	1.093
r_mcbond_it	0.546
r_nbd_refined	0.222
r_symmetry_vdw_refined	0.213
r_symmetry_hbond_refined	0.176
r_xyhbond_nbd_refined	0.152

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_1_deg	5.603
r_scangle_it	3.515
r_scbond_it	2.17
r_angle_refined_deg	1.537
r_mcangle_it	1.093
r_mcbond_it	0.546
r_nbd_refined	0.222
r_symmetry_vdw_refined	0.213
r_symmetry_hbond_refined	0.176
r_xyhbond_nbd_refined	0.152
r_chiral_restr	0.114
r_bond_refined_d	0.013
r_gen_planes_refined	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	7012
Nucleic Acid Atoms
Solvent Atoms	249
Heterogen Atoms	28

Software

Software
Software Name	Purpose
REFMAC	refinement
MAR345	data collection
SCALEPACK	data scaling
CNS	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.