3H4V

Selective screening and design to identify inhibitors of leishmania major pteridine reductase 1


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP5.529312% PEG 5000, 100MM SODIUM ACETATE, 100MM CALCIUM ACETATE, pH 5.50, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.855.5

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 95.206α = 90
b = 103.492β = 108.24
c = 146.476γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 4MIRRORS2003-09-28MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID14-4ESRFID14-4

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
12.43095.50.250.128.12.7100504227
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
2.42.4989.50.6093.1

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 REPLACEMENTTHROUGHOUTPDB ENTRY 1E922.430100504498595.20.280.2760.356RANDOM23.68
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]
-0.38-0.39-0.080.22
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.928
r_dihedral_angle_4_deg20.789
r_dihedral_angle_3_deg17.559
r_dihedral_angle_1_deg7.942
r_scangle_it7.7
r_scbond_it6.772
r_mcangle_it5.108
r_mcbond_it3.27
r_angle_refined_deg1.852
r_symmetry_hbond_refined0.495
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.928
r_dihedral_angle_4_deg20.789
r_dihedral_angle_3_deg17.559
r_dihedral_angle_1_deg7.942
r_scangle_it7.7
r_scbond_it6.772
r_mcangle_it5.108
r_mcbond_it3.27
r_angle_refined_deg1.852
r_symmetry_hbond_refined0.495
r_nbtor_refined0.315
r_symmetry_vdw_refined0.307
r_nbd_refined0.258
r_xyhbond_nbd_refined0.248
r_chiral_restr0.117
r_bond_refined_d0.019
r_gen_planes_refined0.007
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms15900
Nucleic Acid Atoms
Solvent Atoms1098
Heterogen Atoms640

Software

Software
Software NamePurpose
AMoREphasing
REFMACrefinement
HKL-2000data reduction
DENZOdata reduction
SCALEPACKdata scaling