3QMN | pdb_00003qmn

Crystal Structure of 4'-Phosphopantetheinyl Transferase AcpS from Vibrio cholerae O1 biovar eltor

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	4.6	289	30% MPD, 0.1 M Sodium Acetate pH 4.6, 20 mM Calcium Chloride, 5 mM Coenzyme A, VAPOR DIFFUSION, HANGING DROP, temperature 289K

Crystal Properties
Matthews coefficient	Solvent content
2.65	53.66

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 94.553	α = 90
b = 139.039	β = 93.72
c = 138.319	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	CCD	ADSC QUANTUM 315r	mirrors	2009-02-28	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 19-ID	0.9794	APS	19-ID

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	1.85	45.55	99.4	0.091	7.7	3.7	300465	300465			23.36

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	1.85	1.88	99.7		0.54	2	3.7

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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	SAD	THROUGHOUT	1.85	29.89	284976	284976	15148	99.24	0.15791	0.15615	0.1701	0.19127	0.2043	RANDOM	27.607

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]
0.38		0.86	-0.09		-0.19

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	25.431
r_dihedral_angle_3_deg	8.408
r_dihedral_angle_4_deg	8.194
r_scangle_it	4.712
r_scbond_it	2.783
r_dihedral_angle_1_deg	2.241
r_angle_refined_deg	1.755
r_mcangle_it	1.463
r_angle_other_deg	0.854
r_mcbond_it	0.745

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	25.431
r_dihedral_angle_3_deg	8.408
r_dihedral_angle_4_deg	8.194
r_scangle_it	4.712
r_scbond_it	2.783
r_dihedral_angle_1_deg	2.241
r_angle_refined_deg	1.755
r_mcangle_it	1.463
r_angle_other_deg	0.854
r_mcbond_it	0.745
r_mcbond_other	0.229
r_chiral_restr	0.102
r_bond_refined_d	0.012
r_gen_planes_refined	0.005
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	23277
Nucleic Acid Atoms
Solvent Atoms	2487
Heterogen Atoms	1442

Software

Software
Software Name	Purpose
SBC-Collect	data collection
HKL-3000	phasing
SHELXS	phasing
MLPHARE	phasing
RESOLVE	model building
SOLVE	phasing
PHENIX	model building
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling
RESOLVE	phasing
PHENIX	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.