5UBG | pdb_00005ubg

Catalytic core domain of Adenosine triphosphate phosphoribosyltransferase from Campylobacter jejuni with bound Phosphoribosyl-ATP

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5UB9	single chain of PDB 5UB9

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5	293.15	0.1 M sodium acetate pH 5.0, 0.01 M ZnCl2, 7-10% PEG 6000, formed crystals soaked with 5 mM PR-ATP for 30-60 min

Crystal Properties
Matthews coefficient	Solvent content
2.43	50.46

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 67.458	α = 90
b = 80.46	β = 90
c = 92.728	γ = 90

Symmetry
Space Group	P 21 21 21

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	80	CCD	ADSC QUANTUM 210r		2014-04-02	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	AUSTRALIAN SYNCHROTRON BEAMLINE MX1	0.959	Australian Synchrotron	MX1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	CC (Half)	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	1.9	34.55	99.8	0.067	1	23.9	10.8		40502

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.9	1.94	97.1		0.91	0.769	3.2	10.5

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	single chain of PDB 5UB9	1.9	34.55	38357	2085	99.78	0.19764	0.1959	0.18	0.22902	0.21	RANDOM	33.602

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]
-2.33			-0.53		2.87

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.145
r_sphericity_free	18.126
r_dihedral_angle_4_deg	16.947
r_dihedral_angle_3_deg	13.292
r_sphericity_bonded	8.048
r_dihedral_angle_1_deg	5.849
r_long_range_B_other	4.082
r_long_range_B_refined	4.081
r_scangle_other	3.713
r_mcangle_other	3.505
r_mcangle_it	3.504
r_scbond_it	3.223
r_scbond_other	3.194
r_mcbond_it	2.984
r_mcbond_other	2.98
r_rigid_bond_restr	2.21
r_angle_refined_deg	1.431
r_angle_other_deg	0.985
r_chiral_restr	0.079
r_bond_refined_d	0.009
r_gen_planes_refined	0.005
r_bond_other_d	0.004
r_gen_planes_other	0.003
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_scangle_it

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3432
Nucleic Acid Atoms
Solvent Atoms	194
Heterogen Atoms	94

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing