4CLR

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


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2C7VPDB ENTRY 2C7V

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
2.141.39

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 74.346α = 90
b = 90.775β = 115.27
c = 84.378γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315r2011-08-01MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I04DiamondI04

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
11.7529.2990.0817.97.4100986
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)
11.751.8494.80.563.46.6

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 2C7V1.7529.295850511198.870.138880.137240.16917RANDOM17.774
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]
-0.87-0.12.45-1.05
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.994
r_dihedral_angle_4_deg17.436
r_dihedral_angle_3_deg12.919
r_dihedral_angle_1_deg5.788
r_mcangle_it2.187
r_scbond_it1.888
r_angle_refined_deg1.609
r_mcbond_it1.356
r_mcbond_other1.355
r_angle_other_deg0.801
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.994
r_dihedral_angle_4_deg17.436
r_dihedral_angle_3_deg12.919
r_dihedral_angle_1_deg5.788
r_mcangle_it2.187
r_scbond_it1.888
r_angle_refined_deg1.609
r_mcbond_it1.356
r_mcbond_other1.355
r_angle_other_deg0.801
r_chiral_restr0.086
r_bond_refined_d0.013
r_gen_planes_refined0.007
r_bond_other_d0.001
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 Atoms7445
Nucleic Acid Atoms
Solvent Atoms930
Heterogen Atoms240

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing