3IX2

CRYSTAL STRUCTURE OF PURINE NUCLEOSIDE PHOSPHORYLASE FROM MYCOBACTERIUM TUBERCULOSIS IN COMPLEX WITH ACYCLOVIR


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1N3I 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP8293100 mM Tris, pH 8.0, 25%PEG 3350, and 25 mM MgCl2
Crystal Properties
Matthews coefficientSolvent content
1.7931.14

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 105.177α = 90
b = 135.759β = 90
c = 41.434γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMAR scanner 300 mm plate2009-02-02MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONLNLS BEAMLINE D03B-MX11.427LNLSD03B-MX1

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)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
12.133.94900.080.0810739559355592220
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)RedundancyNumber Unique Reflections (All)
2.12.2900.20.2342200

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (I)Cut-off Sigma (F)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT1N3I2.133.94223555931718167993.920.186530.186530.182560.26197RANDOM23.187
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]
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.267
r_dihedral_angle_4_deg21.6
r_dihedral_angle_3_deg18.374
r_dihedral_angle_1_deg8.139
r_scangle_it4.722
r_scbond_it3.124
r_mcangle_it2.923
r_angle_refined_deg2.388
r_mcbond_it1.946
r_symmetry_vdw_refined0.341
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.267
r_dihedral_angle_4_deg21.6
r_dihedral_angle_3_deg18.374
r_dihedral_angle_1_deg8.139
r_scangle_it4.722
r_scbond_it3.124
r_mcangle_it2.923
r_angle_refined_deg2.388
r_mcbond_it1.946
r_symmetry_vdw_refined0.341
r_nbtor_refined0.326
r_chiral_restr0.292
r_nbd_refined0.267
r_symmetry_hbond_refined0.215
r_xyhbond_nbd_refined0.19
r_bond_refined_d0.022
r_gen_planes_refined0.014
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5688
Nucleic Acid Atoms
Solvent Atoms388
Heterogen Atoms63

Software

Software
Software NamePurpose
MAR345dtbdata collection
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
REFMACrefinement