1VMK

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


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1A9O 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION,SITTING DROP,NANODROP6.52770.2M MgCl2, 20.0% PEG-1000, 0.1M Cacodylate pH 6.5, VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
2.5651.64

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 46.478α = 117.34
b = 74.601β = 100.95
c = 74.591γ = 100.71
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDAPSsagitally focusing 2nd crystal, Rosenbaum-Rock vertical focusing mirror2004-02-20MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 19-BMAPS19-BM

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym I (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
1243.3497.720.10612.883.775406130.41
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
122.0793.790.5222.583.435179

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT1a9o2.0143.3451297275597.230.205750.203910.23995RANDOM32.66
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]
1.111.251.40.050.750.52
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.602
r_dihedral_angle_3_deg14.531
r_dihedral_angle_4_deg12.745
r_scangle_it7.09
r_dihedral_angle_1_deg6.321
r_scbond_it5.208
r_mcangle_it2.875
r_mcbond_it2.066
r_angle_refined_deg1.615
r_angle_other_deg0.964
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.602
r_dihedral_angle_3_deg14.531
r_dihedral_angle_4_deg12.745
r_scangle_it7.09
r_dihedral_angle_1_deg6.321
r_scbond_it5.208
r_mcangle_it2.875
r_mcbond_it2.066
r_angle_refined_deg1.615
r_angle_other_deg0.964
r_mcbond_other0.4
r_symmetry_vdw_other0.333
r_symmetry_hbond_refined0.248
r_nbd_refined0.21
r_nbd_other0.199
r_nbtor_refined0.182
r_xyhbond_nbd_refined0.176
r_symmetry_vdw_refined0.136
r_chiral_restr0.096
r_nbtor_other0.089
r_bond_refined_d0.017
r_gen_planes_refined0.007
r_gen_planes_other0.003
r_bond_other_d0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5591
Nucleic Acid Atoms
Solvent Atoms338
Heterogen Atoms34

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMACrefinement