5L4N

Leishmania major Pteridine reductase 1 (PTR1) in complex with compound 1


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2BFA 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP293Protein solution: 12.5 mg/mL in 20 mM Sodium Acetate pH5.3 and 10 mM DTT. Crystallisation buffer: 12% PEG 4600, 100 mM Sodium Acetate buffer pH 5.5 and 120-160 mM Calcium Acetate
Crystal Properties
Matthews coefficientSolvent content
2.6152.9

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 94.699α = 90
b = 104.25β = 90
c = 137.04γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M-F2014-10-18MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I040.9795DiamondI04

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge 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
12.3594.795.30.1297.53.454151217.2
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)
12.352.4897.10.4312.73.3

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 REPLACEMENTTHROUGHOUT2BFA2.3582.9751393271494.610.165740.163030.2178RANDOM24.154
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]
-0.020.010.01
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.979
r_dihedral_angle_4_deg18.159
r_dihedral_angle_3_deg14.085
r_dihedral_angle_1_deg6.765
r_long_range_B_refined6.18
r_mcangle_it3.481
r_scbond_it2.492
r_mcbond_it2.162
r_angle_refined_deg1.878
r_chiral_restr0.112
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.979
r_dihedral_angle_4_deg18.159
r_dihedral_angle_3_deg14.085
r_dihedral_angle_1_deg6.765
r_long_range_B_refined6.18
r_mcangle_it3.481
r_scbond_it2.492
r_mcbond_it2.162
r_angle_refined_deg1.878
r_chiral_restr0.112
r_bond_refined_d0.017
r_gen_planes_refined0.009
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_it
r_scangle_other
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms7588
Nucleic Acid Atoms
Solvent Atoms563
Heterogen Atoms266

Software

Software
Software NamePurpose
REFMACrefinement
iMOSFLMdata reduction
SCALAdata scaling
MOLREPphasing