4CL8

Crystal structure of pteridine reductase 1 (PTR1) from Trypanosoma brucei in ternary complex with cofactor and inhibitor


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1RESERVOIR CONTAINED 1.7-2.7 M SODIUM ACETATE, 20-50 MM SODIUM CITRATE PH 4.5-5.0
Crystal Properties
Matthews coefficientSolvent content
2.0138.88

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 74.43α = 90
b = 89.42β = 115.53
c = 82.22γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100RIGAKU R-AXIS IV IMAGING PLATE2011-03-21MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU MICROMAX-007 HF

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
12.244.711000.1967.43.249452
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)
12.22.321000.6633.2

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 DIFFRACTIONOTHERTHROUGHOUTNONE2.234.3746913251199.880.151680.148740.20696RANDOM19.555
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]
-1.54-0.572.65-0.57
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.887
r_dihedral_angle_4_deg17.837
r_dihedral_angle_3_deg15.052
r_dihedral_angle_1_deg6.375
r_angle_other_deg2.991
r_mcangle_it2.281
r_angle_refined_deg1.787
r_scbond_it1.682
r_mcbond_it1.382
r_mcbond_other1.382
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.887
r_dihedral_angle_4_deg17.837
r_dihedral_angle_3_deg15.052
r_dihedral_angle_1_deg6.375
r_angle_other_deg2.991
r_mcangle_it2.281
r_angle_refined_deg1.787
r_scbond_it1.682
r_mcbond_it1.382
r_mcbond_other1.382
r_chiral_restr0.086
r_bond_refined_d0.013
r_gen_planes_refined0.008
r_bond_other_d0.002
r_gen_planes_other0.001
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_mcangle_other
r_scbond_other
r_scangle_it
r_scangle_other
r_long_range_B_refined
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 Atoms7457
Nucleic Acid Atoms
Solvent Atoms606
Heterogen Atoms292

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling