3BF1 | pdb_00003bf1

Type III pantothenate kinase from Thermotoga maritima complexed with pantothenate and ADP

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		277	16% PEG 3350, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.19	43.84

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 74.962	α = 90
b = 136.685	β = 109.71
c = 75.01	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++			M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU FR-E+ SUPERBRIGHT	1.5418

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	2.3	50	98.9	0.066				58933

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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	2.3	50	58933	3156	98.63	0.19363	0.19027	0.19	0.25696	0.25	RANDOM	21.275

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]
0.2		0.19	-0.2		0.13

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.404
r_dihedral_angle_4_deg	20.046
r_dihedral_angle_3_deg	15.339
r_dihedral_angle_1_deg	5.398
r_scangle_it	1.973
r_angle_refined_deg	1.409
r_scbond_it	1.141
r_mcangle_it	0.853
r_mcbond_it	0.497
r_nbtor_refined	0.302
r_symmetry_hbond_refined	0.233
r_symmetry_vdw_refined	0.2
r_nbd_refined	0.189
r_chiral_restr	0.159
r_xyhbond_nbd_refined	0.146
r_bond_refined_d	0.009
r_gen_planes_refined	0.003
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	11574
Nucleic Acid Atoms
Solvent Atoms	648
Heterogen Atoms	252

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-2000	data collection
HKL-2000	data reduction
HKL-2000	data scaling