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Crystal structure of pteridine reductase 1 (PTR1) from Trypanosoma brucei in ternary complex with cofactor and inhibitor
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2C7V PDB ENTRY 2C7V
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 RESERVOIR CONTAINED 1.7-2.7 M SODIUM ACETATE, 20-50 MM SODIUM CITRATE PH 4.5-5.0
Crystal Properties Matthews coefficient Solvent content 2.1 41.39
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 74.346 α = 90 b = 90.775 β = 115.27 c = 84.378 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 CCD ADSC QUANTUM 315r 2011-08-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 Diamond I04
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 1.75 29.2 99 0.08 17.9 7.4 100986
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 1.75 1.84 94.8 0.56 3.4 6.6
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 PDB ENTRY 2C7V 1.75 29.2 95850 5111 98.87 0.13888 0.13724 0.1518 0.16917 0.1797 RANDOM 17.774
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 -0.1 2.45 -1.05
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.994 r_dihedral_angle_4_deg 17.436 r_dihedral_angle_3_deg 12.919 r_dihedral_angle_1_deg 5.788 r_mcangle_it 2.187 r_scbond_it 1.888 r_angle_refined_deg 1.609 r_mcbond_it 1.356 r_mcbond_other 1.355 r_angle_other_deg 0.801
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.994 r_dihedral_angle_4_deg 17.436 r_dihedral_angle_3_deg 12.919 r_dihedral_angle_1_deg 5.788 r_mcangle_it 2.187 r_scbond_it 1.888 r_angle_refined_deg 1.609 r_mcbond_it 1.356 r_mcbond_other 1.355 r_angle_other_deg 0.801 r_chiral_restr 0.086 r_bond_refined_d 0.013 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001 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 Atoms Number Protein Atoms 7445 Nucleic Acid Atoms Solvent Atoms 930 Heterogen Atoms 240
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling MOLREP phasing