4CLD

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
2.0539.86

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 74.769α = 90
b = 90.056β = 115.75
c = 82.747γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100RIGAKU R-AXIS IV IMAGING PLATE2011-05-23MSINGLE 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
11.7719.7492.10.0717.7587724
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)
11.771.87780.433.74.6

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 2C7V1.7719.7483242444591.910.145810.143820.18309RANDOM17.371
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]
-0.91-0.382.64-1.05
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.15
r_dihedral_angle_4_deg17.851
r_dihedral_angle_3_deg13.493
r_dihedral_angle_1_deg5.904
r_mcangle_it2.102
r_scbond_it1.782
r_angle_refined_deg1.603
r_mcbond_it1.305
r_mcbond_other1.304
r_angle_other_deg0.816
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.15
r_dihedral_angle_4_deg17.851
r_dihedral_angle_3_deg13.493
r_dihedral_angle_1_deg5.904
r_mcangle_it2.102
r_scbond_it1.782
r_angle_refined_deg1.603
r_mcbond_it1.305
r_mcbond_other1.304
r_angle_other_deg0.816
r_chiral_restr0.085
r_bond_refined_d0.012
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 Atoms7465
Nucleic Acid Atoms
Solvent Atoms883
Heterogen Atoms272

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing