2H1Y

Crystal structure of malonyl-CoA:Acyl carrier protein transacylase (MCAT) from Helicobacter pylori

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8	277	0.1M Hepes, 10% v/v PEG10000, 8% v/v MPD, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.27	45.81

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 43.616	α = 90
b = 76.175	β = 101.22
c = 99.768	γ = 90

Symmetry
Space Group	P 1 21 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	IMAGE PLATE	RIGAKU RAXIS IV		2006-03-15	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU	1.5418

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	2.5	50	99.8	0.065	0.065	14.2	3.7		22318

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	2.5	2.59	100		0.452	0.452	2.8	3.6	2234

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 (All)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 1NM2	2.5	36.7	22004	1126	98.29	0.217	0.215	0.262	RANDOM	55.749

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]
2.26		0.45	-0.73		-1.36

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	41.988
r_dihedral_angle_4_deg	22.89
r_dihedral_angle_3_deg	20.301
r_dihedral_angle_1_deg	5.533
r_scangle_it	2.319
r_scbond_it	1.429
r_angle_refined_deg	1.409
r_mcangle_it	1.075
r_mcbond_it	0.607
r_nbtor_refined	0.304

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	41.988
r_dihedral_angle_4_deg	22.89
r_dihedral_angle_3_deg	20.301
r_dihedral_angle_1_deg	5.533
r_scangle_it	2.319
r_scbond_it	1.429
r_angle_refined_deg	1.409
r_mcangle_it	1.075
r_mcbond_it	0.607
r_nbtor_refined	0.304
r_nbd_refined	0.229
r_symmetry_hbond_refined	0.213
r_symmetry_vdw_refined	0.184
r_xyhbond_nbd_refined	0.142
r_chiral_restr	0.101
r_bond_refined_d	0.011
r_gen_planes_refined	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4852
Nucleic Acid Atoms
Solvent Atoms	26
Heterogen Atoms

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
CrystalClear	data reduction
CNS	phasing

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.