5VJP | pdb_00005vjp

Crystal Structure of Adenine Phosphoribosyltransferase from Saccharomyces cerevisiae Complexed with L-2,5-Dideoxy-2,5-Imino-Altritol 1,6-Bisphosphate (L-DIAB) and Adenine

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1G2Q	PDB entry 1G2Q

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		295	100 mM sodium acetate, 0.2 M ammonium sulfate, 22% PEG4000

Crystal Properties
Matthews coefficient	Solvent content
2.99	58.8

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 138.087	α = 90
b = 49.219	β = 130.55
c = 95.354	γ = 90

Symmetry
Space Group	C 1 2 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	RAYONIX MX-225HE		2017-02-09	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 31-ID	0.97931	APS	31-ID

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	1.98	72.45	98.7	0.12	1	7.9	3.7		33741			26

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.98	2.03	99.9		0.77	2	3.7

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 1G2Q	1.98	72.45	31993	1727	98.55	0.26295	0.26194	0.27	0.28079	0.29	RANDOM	40.204

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]
3.78		2.41	-4.07		-1.55

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.586
r_dihedral_angle_4_deg	14.38
r_dihedral_angle_3_deg	14.092
r_dihedral_angle_1_deg	6.168
r_long_range_B_refined	4.173
r_long_range_B_other	4.172
r_mcangle_it	2.207
r_mcangle_other	2.207
r_scangle_other	2.066
r_mcbond_it	1.31
r_mcbond_other	1.307
r_angle_refined_deg	1.247
r_scbond_it	1.214
r_scbond_other	1.213
r_angle_other_deg	0.873
r_chiral_restr	0.067
r_bond_refined_d	0.007
r_gen_planes_refined	0.004
r_bond_other_d	0.002
r_gen_planes_other	0.001
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
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2718
Nucleic Acid Atoms
Solvent Atoms	181
Heterogen Atoms	76

Software

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