3BMC

Structure of Pteridine Reductase 1 (PTR1) from Trypanosoma brucei in ternary complex with cofactor (NADP+) and substrate (folate)


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP4.52932-3M sodium acetate, 10-100mM sodium citrate, pH 4.5, vapor diffusion, hanging drop, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
1.9837.93

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 74.441α = 90
b = 88.596β = 115.34
c = 81.587γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS IVmirrorsSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU MICROMAX-0071.54

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)R Sym 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
12.673.73781.10.0680.0689.12.223556
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.62.74740.3770.37722.33152

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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 REPLACEMENTTHROUGHOUT2.637.6723539122479.490.1920.1890.244RANDOM30.712
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]
-4.56-2.837.48-5.34
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.998
r_dihedral_angle_4_deg18.618
r_dihedral_angle_3_deg17.034
r_dihedral_angle_1_deg5.444
r_angle_refined_deg1.46
r_scangle_it1.239
r_scbond_it0.92
r_mcangle_it0.548
r_symmetry_hbond_refined0.418
r_symmetry_vdw_refined0.366
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.998
r_dihedral_angle_4_deg18.618
r_dihedral_angle_3_deg17.034
r_dihedral_angle_1_deg5.444
r_angle_refined_deg1.46
r_scangle_it1.239
r_scbond_it0.92
r_mcangle_it0.548
r_symmetry_hbond_refined0.418
r_symmetry_vdw_refined0.366
r_mcbond_it0.331
r_nbtor_refined0.303
r_xyhbond_nbd_refined0.286
r_nbd_refined0.207
r_chiral_restr0.097
r_bond_refined_d0.009
r_gen_planes_refined0.004
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms7405
Nucleic Acid Atoms
Solvent Atoms253
Heterogen Atoms320

Software

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