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Structure of Trypanosoma brucei pteridine reductase (PTR1) in ternary complex with cofactor and the antifolate methotrexate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1E92 PBD ENTRY 1E92
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 PROTEIN BUFFER WAS 20 MM TRIS HCL, PH 7.0 WITH 1MM NADP, 1 MM METHOTREXATE AND 20 MM DITHIOTHREITOL, PROTEIN CONCENTRATION WAS 6 MG/ML. HANGING DROP RESERVOIR SOLUTION WAS 0.1 M SODIUM CACODYLATE PH 6.5 AND 1.4 M SODIUM ACETATE.
Crystal Properties Matthews coefficient Solvent content 2.01 38.22
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 74.655 α = 90 b = 90.244 β = 115.76 c = 82.841 γ = 90
Symmetry Space Group P 1 21 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 IMAGE PLATE RIGAKU IMAGE PLATE MIRRORS 2004-07-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 2.2 74.5 99.2 0.06 12.4 2.8 50048
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.2 2.26 93.1 0.17 3.5 2.1
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PBD ENTRY 1E92 2.2 74.54 47369 2534 99.2 0.157 0.153 0.1539 0.223 0.2217 RANDOM 24.22
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] -1.87 -0.58 2.67 -1.31
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.424 r_dihedral_angle_4_deg 20.819 r_dihedral_angle_3_deg 16.943 r_dihedral_angle_1_deg 5.763 r_scangle_it 2.349 r_scbond_it 1.466 r_angle_refined_deg 1.402 r_mcangle_it 1.026 r_mcbond_it 0.584 r_chiral_restr 0.538
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.424 r_dihedral_angle_4_deg 20.819 r_dihedral_angle_3_deg 16.943 r_dihedral_angle_1_deg 5.763 r_scangle_it 2.349 r_scbond_it 1.466 r_angle_refined_deg 1.402 r_mcangle_it 1.026 r_mcbond_it 0.584 r_chiral_restr 0.538 r_nbtor_refined 0.297 r_symmetry_vdw_refined 0.229 r_nbd_refined 0.201 r_symmetry_hbond_refined 0.159 r_xyhbond_nbd_refined 0.154 r_bond_refined_d 0.013 r_gen_planes_refined 0.004 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_mcangle_other r_scbond_other 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 Atoms Number Protein Atoms 7648 Nucleic Acid Atoms Solvent Atoms 799 Heterogen Atoms 334
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling MOLREP phasing