4G5F

Pantothenate synthetase in complex with racemate (2S)-2,3-DIHYDRO-1,4-BENZODIOXINE-2-CARBOXYLIC ACID and (2R)-2,3-DIHYDRO-1,4-BENZODIOXINE-2-CARBOXYLIC ACID

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8	293	11-14% w/v PEG3000, 150 mM lithium sulfate, 100 mM imidazole, 2% v/v ethanol, 10% v/v glycerol, 20 mM magnesium chloride, pH 8, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.12	42.04

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 48.41	α = 90
b = 70.99	β = 99.58
c = 81.68	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					M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X06DA	0.97	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	2.33	47.73	98.6	0.113	7.5	3.6	83193	23179			31.7

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	2.33	2.46	90.7		0.477	2.6	3.3	10122

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	3COV	2.33	47.73	21974	1191	98.61	0.17382	0.17012	0.2399	RANDOM	31.857

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]
0.94		1.32	1.72		-2.22

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.914
r_dihedral_angle_4_deg	16.881
r_dihedral_angle_3_deg	16.27
r_dihedral_angle_1_deg	6.255
r_scangle_it	4.216
r_scbond_it	2.633
r_mcangle_it	1.701
r_angle_refined_deg	1.661
r_mcbond_it	0.935
r_chiral_restr	0.107
r_bond_refined_d	0.018
r_gen_planes_refined	0.009
r_angle_other_deg
r_gen_planes_other
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
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	4076
Nucleic Acid Atoms
Solvent Atoms	216
Heterogen Atoms	78

Software

Software
Software Name	Purpose
REFMAC	refinement