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Crystal Structure of Trypanosoma brucei DHFR in complex with the cofactor and inhibitor P25
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3RG9
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 MICROBATCH 6.5 293 35% w/v PEG4000, 50 mM ammonium sulfate, 50 mM bis-tris, pH 6.5
Crystal Properties Matthews coefficient Solvent content 1.6 23.28
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 41.92 α = 90 b = 60.928 β = 90 c = 68.882 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS PILATUS 6M 2023-03-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I24 0.99989 Diamond I24
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) 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 2.9 60.93 100 0.124 0.147 0.077 0.996 8.6 6.3 4243 2 25.2
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.9 3.08 100 0.964 1.134 0.592 0.92 2.1 6.6
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 2.9 45.64 4027 186 99.98 0.19274 0.18778 0.1908 0.29797 0.2981 RANDOM 75.303
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] 0.08 0.01 -0.09
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 16.554 r_long_range_B_refined 15.694 r_mcangle_it 9.543 r_dihedral_angle_1_deg 7.097 r_scbond_it 6.065 r_dihedral_angle_2_deg 6.003 r_mcbond_it 5.787 r_angle_refined_deg 1.581 r_chiral_restr 0.119 r_gen_planes_refined 0.007
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 16.554 r_long_range_B_refined 15.694 r_mcangle_it 9.543 r_dihedral_angle_1_deg 7.097 r_scbond_it 6.065 r_dihedral_angle_2_deg 6.003 r_mcbond_it 5.787 r_angle_refined_deg 1.581 r_chiral_restr 0.119 r_gen_planes_refined 0.007 r_bond_refined_d 0.004 r_bond_other_d r_angle_other_deg r_dihedral_angle_4_deg r_gen_planes_other 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_mcbond_other r_mcangle_other r_scbond_other r_scangle_it r_scangle_other 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 1612 Nucleic Acid Atoms Solvent Atoms 23 Heterogen Atoms 66
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling MOLREP phasing