3IUE | pdb_00003iue

Crystal structure of pantothenate synthetase in complex with 2-(5-methoxy-2-(5-Methylpyridin-2-ylsulfonylcarbamoyl)-1H-indol-1-yl) acetic acid

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3COW	PDB ENTRY 3COW

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8	293	12-14% PEG 3000, 100-150 mM Li2SO4, 100-150 mM imidazole, 2-4% Ethanol, 5-10% Glycerol,20 mM MgCl2, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.2	43.97

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 48.55	α = 90
b = 70.71	β = 99.37
c = 81.84	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	MARMOSAIC 225 mm CCD		2009-02-18	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X06DA	0.99	SLS	X06DA

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	1.73	27.68	99.9	0.079	11.9	3.7		57085			19.5

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	1.73	1.82	100		0.539	2.1	3.6	8321

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 (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 3COW	1.73	27.68	54175	2891	99.93	0.1743	0.17247	0.17	0.20755	0.21	RANDOM	22.212

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]
0.42		-0.58	0.74		-1.35

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.264
r_dihedral_angle_4_deg	16.251
r_dihedral_angle_3_deg	14.433
r_dihedral_angle_1_deg	5.771
r_scangle_it	3.476
r_scbond_it	2.162
r_angle_refined_deg	1.49
r_mcangle_it	1.455
r_mcbond_it	0.91
r_nbtor_refined	0.306
r_symmetry_vdw_refined	0.257
r_nbd_refined	0.218
r_symmetry_hbond_refined	0.186
r_xyhbond_nbd_refined	0.152
r_chiral_restr	0.092
r_bond_refined_d	0.014
r_gen_planes_refined	0.005
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4159
Nucleic Acid Atoms
Solvent Atoms	570
Heterogen Atoms	172

Software

Software
Software Name	Purpose
PHASES	phasing
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling