3JQG

Crystal structure of pteridine reductase 1 (PTR1) from Trypanosoma brucei in ternary complex with cofactor (NADP+) and inhibitor 6-[(4-methoxybenzyl)sulfanyl]pyrimidine-2,4-diamine (AX6)


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION2932-3M Sodium acetate, 10-100mM Sodium citrate, pH 4.0-6.0, VAPOR DIFFUSION, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.0339.4

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 74.531α = 90
b = 89.845β = 115.53
c = 82.437γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCDPt coated mirrors in a Kirkpatrick-Baez (KB) geometry2006-05-20MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID23-20.87300ESRFID23-2

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
11.953.296.50.0922.474417
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)
11.92.010.291.92.7

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 2C7V1.953.274400373896.270.2140.2110.267RANDOM17.855
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]
-2.9-1.193.07-1.2
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.048
r_dihedral_angle_4_deg17.36
r_dihedral_angle_3_deg14.812
r_dihedral_angle_1_deg5.9
r_scangle_it4.533
r_scbond_it3.687
r_mcangle_it2.497
r_mcbond_it1.681
r_angle_refined_deg1.531
r_nbtor_refined0.302
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.048
r_dihedral_angle_4_deg17.36
r_dihedral_angle_3_deg14.812
r_dihedral_angle_1_deg5.9
r_scangle_it4.533
r_scbond_it3.687
r_mcangle_it2.497
r_mcbond_it1.681
r_angle_refined_deg1.531
r_nbtor_refined0.302
r_symmetry_vdw_refined0.262
r_nbd_refined0.209
r_xyhbond_nbd_refined0.201
r_symmetry_hbond_refined0.181
r_chiral_restr0.095
r_bond_refined_d0.014
r_gen_planes_refined0.006
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms7406
Nucleic Acid Atoms
Solvent Atoms612
Heterogen Atoms264

Software

Software
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACTdata extraction
MAR345data collection