2REF | pdb_00002ref

Crystal structure of the loading GNATL domain of CurA from Lyngbya majuscula soaked with malonyl-CoA

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2REE	Apo CurA GNATL domain

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		277.15	Mother liquor: 100 mM Bis-Tris pH 6.8, 100 mM NaCl, 1.5 M ammonium sulfate, 20% glycerol. Protein buffer: 20 mM Tris pH 7.9, 500 mM NaCl, 10% glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 277.15K

Crystal Properties
Matthews coefficient	Solvent content
3.28	62.5

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 91.886	α = 90
b = 91.886	β = 90
c = 139.486	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	MARMOSAIC 300 mm CCD	K-B pair of biomorph mirrors for vertical and horizontal focusing	2006-06-06	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 23-ID-B	0.97939	APS	23-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	2.75	46.5	99.9	0.094	10.6	9.7	18214	18214	1	1	60.3

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	2.75	2.85	99.9		0.534	4.9	9.8	1800

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 (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION		THROUGHOUT	Apo CurA GNATL domain	2.75	46.5	18193	18190	914	99.8	0.21	0.207	0.24	0.251	0.27	RANDOM	39.054

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]
0.13	0.07		0.13		-0.2

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.381
r_dihedral_angle_3_deg	16.645
r_dihedral_angle_4_deg	14.216
r_dihedral_angle_1_deg	5.59
r_scangle_it	1.561
r_angle_refined_deg	1.351
r_scbond_it	0.915
r_mcangle_it	0.562
r_nbtor_refined	0.305
r_mcbond_it	0.304

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.381
r_dihedral_angle_3_deg	16.645
r_dihedral_angle_4_deg	14.216
r_dihedral_angle_1_deg	5.59
r_scangle_it	1.561
r_angle_refined_deg	1.351
r_scbond_it	0.915
r_mcangle_it	0.562
r_nbtor_refined	0.305
r_mcbond_it	0.304
r_nbd_refined	0.213
r_symmetry_vdw_refined	0.175
r_xyhbond_nbd_refined	0.126
r_symmetry_hbond_refined	0.098
r_chiral_restr	0.093
r_bond_refined_d	0.008
r_gen_planes_refined	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3310
Nucleic Acid Atoms
Solvent Atoms	4
Heterogen Atoms	102

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
Blu-Ice	data collection
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.