5UGF | pdb_00005ugf

Crystal structure of human purine nucleoside phosphorylase (F159Y) mutant complexed with DADMe-ImmG and phosphate

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	295	100 mM HEPES, pH 7.5, 0.2 M lithium sulfate, 25% w/v PEG3350

Crystal Properties
Matthews coefficient	Solvent content
2.08	40.88

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 104.96	α = 90
b = 124.27	β = 90
c = 136.73	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	100	CCD	RAYONIX MX225HE		2016-10-18	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	2.2	69.26	100	0.17	0.99	5.8	6.6		91303			24

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	2.2	2.24	100		0.71	1.8	6

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 3PHB	2.2	69.26	86719	4492	99.96	0.21503	0.21382	0.22	0.23809	0.24	RANDOM	34.993

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]
2.72			-1.13		-1.59

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.537
r_dihedral_angle_3_deg	13.746
r_dihedral_angle_4_deg	12.032
r_long_range_B_refined	6.501
r_long_range_B_other	6.501
r_dihedral_angle_1_deg	6.178
r_mcangle_it	3.195
r_mcangle_other	3.195
r_scangle_other	2.526
r_mcbond_it	1.78
r_mcbond_other	1.78
r_scbond_it	1.429
r_scbond_other	1.429
r_angle_refined_deg	1.368
r_angle_other_deg	0.931
r_chiral_restr	0.075
r_bond_refined_d	0.009
r_gen_planes_refined	0.005
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	13348
Nucleic Acid Atoms
Solvent Atoms	713
Heterogen Atoms	265

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
MOSFLM	data reduction
Aimless	data scaling
PHASER	phasing