3BGS | pdb_00003bgs

Structure of human purine nucleoside phosphorylase with L-DADMe-ImmH and phosphate

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1RR6

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5	291	0.1 M Sodium citrate pH 5.0, 2.3 M ammonium dihydrogenphosphate, Vapor diffusion, sitting drop, temperature 291K

Crystal Properties
Matthews coefficient	Solvent content
4.82	74.27

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 142.801	α = 90
b = 142.801	β = 90
c = 167.348	γ = 120

Symmetry
Space Group	H 3 2

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		2007-11-05	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS BEAMLINE X29A	0.9793	NSLS	X29A

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (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	2.099	99.5	100	0.074	0.076	13.6	12.5	38397	38397

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	2.099	2.18	100		0.714	0.627	2.5	7.7	3798

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		THROUGHOUT	1RR6	2.099	99.5	38395	1922	99.89	0.219	0.218	0.2128	0.249	0.2243	RANDOM	56.149

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]
0.06	0.03		0.06		-0.1

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.793
r_dihedral_angle_4_deg	17.455
r_dihedral_angle_3_deg	14.493
r_dihedral_angle_1_deg	4.891
r_mcangle_it	4.711
r_scangle_it	4.634
r_mcbond_it	3.392
r_scbond_it	3.301
r_angle_refined_deg	1.639
r_nbtor_refined	0.327
r_nbd_refined	0.239
r_xyhbond_nbd_refined	0.211
r_symmetry_hbond_refined	0.191
r_symmetry_vdw_refined	0.172
r_chiral_restr	0.114
r_bond_refined_d	0.015
r_gen_planes_refined	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2299
Nucleic Acid Atoms
Solvent Atoms	101
Heterogen Atoms	34

Software

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