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Crystal structure of trimethoprim-resistant type II dihydrofolate reductase in complex with a bisbenzimidazole inhibitor
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2RH2
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 277 The protein concentration was adjusted from 13.3 mg/ml to 10 mg/mL by addition of a final concentration of 25% MPD. Reservoirs were prepared in Eppendorf tubes with 100mM Tris-Cl pH 8.0 55% MPD in a Greiner 24-well hanging-drop crystallization plate. On a siliconized glass cover slip (Hampton Research), 2.0 uL of protein solution were combined with 2.0 uL of the reservoir solution. The plate was incubated at 277 K, and crystals were obtained after 3-4 days.
Crystal Properties Matthews coefficient Solvent content 2.21 44.24
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 67.617 α = 90 b = 67.617 β = 90 c = 51.977 γ = 90
Symmetry Space Group I 41 2 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 93 CCD RIGAKU SATURN 944+ VariMax HF 2014-09-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 HF 1.54
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 50 94.3 0.204 0.205 0.02 4.6 79.2 6007
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.75 1.78 48.7 0.697 1.5
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 2RH2 1.75 47.86 5681 319 94.27 0.1785 0.1768 0.1891 0.2082 0.221 RANDOM 21.063
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] 0.12 0.12 -0.25
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.412 r_dihedral_angle_3_deg 16.031 r_dihedral_angle_4_deg 14.721 r_dihedral_angle_1_deg 6.246 r_angle_refined_deg 2.061 r_angle_other_deg 0.947 r_chiral_restr 0.111 r_bond_refined_d 0.02 r_gen_planes_refined 0.01 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.412 r_dihedral_angle_3_deg 16.031 r_dihedral_angle_4_deg 14.721 r_dihedral_angle_1_deg 6.246 r_angle_refined_deg 2.061 r_angle_other_deg 0.947 r_chiral_restr 0.111 r_bond_refined_d 0.02 r_gen_planes_refined 0.01 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 418 Nucleic Acid Atoms Solvent Atoms 60 Heterogen Atoms 26
Software Software Software Name Purpose HKL-2000 data reduction HKL-2000 data scaling REFMAC refinement PDB_EXTRACT data extraction REFMAC phasing