3GIT | pdb_00003git

Crystal structure of a truncated acetyl-CoA synthase

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1OAO	PDB ENTRY 1OAO: ACS domain 2 (320-470) and domain 3 (500-729)

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.1	298	ammonium sulfate, pH 7.1, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
3.42	64.02

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 166.4	α = 90
b = 166.4	β = 90
c = 245.2	γ = 120

Symmetry
Space Group	P 31 2 1

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		2004-09-12	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE BM30A	1.008	ESRF	BM30A

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	3	20	99.5	0.053	19.6	7.5	78758	78342		-3	51.823

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	3	3.1	99.7		0.243	6.3	7.5	7323

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 1OAO: ACS domain 2 (320-470) and domain 3 (500-729)	3	19.98	78758	78314	3902	99.47	0.173	0.173	0.171	0.18	0.208	0.21	RANDOM	57.237

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]
-1.83	-0.92		-1.83		2.75

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.522
r_dihedral_angle_4_deg	19.873
r_dihedral_angle_3_deg	18.452
r_dihedral_angle_1_deg	6.316
r_scangle_it	1.734
r_angle_refined_deg	1.586
r_scbond_it	1.07
r_mcangle_it	0.597
r_mcbond_it	0.369
r_symmetry_vdw_refined	0.35

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.522
r_dihedral_angle_4_deg	19.873
r_dihedral_angle_3_deg	18.452
r_dihedral_angle_1_deg	6.316
r_scangle_it	1.734
r_angle_refined_deg	1.586
r_scbond_it	1.07
r_mcangle_it	0.597
r_mcbond_it	0.369
r_symmetry_vdw_refined	0.35
r_nbtor_refined	0.32
r_nbd_refined	0.226
r_xyhbond_nbd_refined	0.146
r_symmetry_hbond_refined	0.136
r_chiral_restr	0.106
r_bond_refined_d	0.015
r_gen_planes_refined	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	19742
Nucleic Acid Atoms
Solvent Atoms	189
Heterogen Atoms	216

Software

Software
Software Name	Purpose
XSCALE	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
Xnemo	data collection
XDS	data reduction

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.