3GGS | pdb_00003ggs

Human purine nucleoside phosphorylase double mutant E201Q,N243D complexed with 2-fluoro-2'-deoxyadenosine

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3GB9	PDB entry 3GB9

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	4.6	298	1.54M Ammonium sulfate, 0.05M Sodium potassium phosphate pH 6.8, 3% Trimethylamine N-oxide, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
3.37	63.49

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 71.24	α = 90
b = 130.646	β = 90
c = 149.433	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	ADSC QUANTUM 315		2008-06-23	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 24-ID-C	0.9793	APS	24-ID-C

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	2.5	50	99.4	0.09	17.887	6.6		47561		-3	57.2

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	2.5	2.59	98.1		0.39		6.4	4622

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	FOURIER SYNTHESIS	THROUGHOUT	PDB entry 3GB9	2.52	50	47486	2395	98.59	0.214	0.212	0.22	0.251	0.26	RANDOM	52.026

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]
8.33			-3.53		-4.81

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.721
r_dihedral_angle_3_deg	19.394
r_dihedral_angle_4_deg	17.466
r_dihedral_angle_1_deg	6.352
r_mcangle_it	2.381
r_scangle_it	2.091
r_scbond_it	1.444
r_mcbond_it	1.402
r_angle_refined_deg	1.26
r_angle_other_deg	0.88

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.721
r_dihedral_angle_3_deg	19.394
r_dihedral_angle_4_deg	17.466
r_dihedral_angle_1_deg	6.352
r_mcangle_it	2.381
r_scangle_it	2.091
r_scbond_it	1.444
r_mcbond_it	1.402
r_angle_refined_deg	1.26
r_angle_other_deg	0.88
r_mcbond_other	0.373
r_chiral_restr	0.07
r_bond_refined_d	0.009
r_gen_planes_refined	0.005
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6614
Nucleic Acid Atoms
Solvent Atoms	64
Heterogen Atoms	226

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
REFMAC	phasing

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.