1VMK | pdb_00001vmk

Crystal structure of Purine nucleoside phosphorylase (TM1596) from Thermotoga maritima at 2.01 A resolution

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1A9O

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION,SITTING DROP,NANODROP	6.5	277	0.2M MgCl2, 20.0% PEG-1000, 0.1M Cacodylate pH 6.5, VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.56	51.64

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 46.478	α = 117.34
b = 74.601	β = 100.95
c = 74.591	γ = 100.71

Symmetry
Space Group	P 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	APS	sagitally focusing 2nd crystal, Rosenbaum-Rock vertical focusing mirror	2004-02-20	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 19-BM		APS	19-BM

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	43.34	97.72	0.106	12.88	3.77		54061			30.41

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2	2.07	93.79		0.522	2.58	3.43	5179

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	1a9o	2.01	43.34	51297	2755	97.23	0.20575	0.20391	0.22	0.23995	0.25	RANDOM	32.66

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]
1.11	1.25	1.4	0.05	0.75	0.52

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.602
r_dihedral_angle_3_deg	14.531
r_dihedral_angle_4_deg	12.745
r_scangle_it	7.09
r_dihedral_angle_1_deg	6.321
r_scbond_it	5.208
r_mcangle_it	2.875
r_mcbond_it	2.066
r_angle_refined_deg	1.615
r_angle_other_deg	0.964
r_mcbond_other	0.4
r_symmetry_vdw_other	0.333
r_symmetry_hbond_refined	0.248
r_nbd_refined	0.21
r_nbd_other	0.199
r_nbtor_refined	0.182
r_xyhbond_nbd_refined	0.176
r_symmetry_vdw_refined	0.136
r_chiral_restr	0.096
r_nbtor_other	0.089
r_bond_refined_d	0.017
r_gen_planes_refined	0.007
r_gen_planes_other	0.003
r_bond_other_d	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5591
Nucleic Acid Atoms
Solvent Atoms	338
Heterogen Atoms	34

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
MOLREP	phasing
REFMAC	refinement