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X-ray structure of Escherichia coli dihydrofolate reductase L28R mutant in complex with trimethoprim
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other WT DHFR solved in the same space group
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.6 293 0.1 M sodium citrate tribasic dihydrate (pH 5.6), 0.15 M ammonium acetate and 17.5% or 20% PEG 4000;
10 mM NADPH, 2 mM TMP was incubated with the L28R variant of DHFR overnight at 293 K
Crystal Properties Matthews coefficient Solvent content 3.03 59.39
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 61.548 α = 90 b = 61.548 β = 90 c = 104.661 γ = 120
Symmetry Space Group P 32 2 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 PIXEL DECTRIS PILATUS 6M 2018-07-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID 0.97919 APS 19-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.1 50 99.9 0.076 0.025 1 37.5 9.3 13880 -3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.1 2.12 100 8.94 3.012 0.672 0.7 8.8
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 Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT WT DHFR solved in the same space group 2.1 37.37 9837 70.95 0.2493 0.2493 0.2537 0.2779 FULL CROSS VALIDATION 35.198
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] -0.11 -0.05 -0.11 0.35
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.498 r_dihedral_angle_3_deg 18.538 r_dihedral_angle_4_deg 13.371 r_dihedral_angle_1_deg 7.56 r_angle_refined_deg 1.417 r_angle_other_deg 1.112 r_chiral_restr 0.054 r_bond_refined_d 0.006 r_gen_planes_refined 0.006 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.498 r_dihedral_angle_3_deg 18.538 r_dihedral_angle_4_deg 13.371 r_dihedral_angle_1_deg 7.56 r_angle_refined_deg 1.417 r_angle_other_deg 1.112 r_chiral_restr 0.054 r_bond_refined_d 0.006 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1271 Nucleic Acid Atoms Solvent Atoms 131 Heterogen Atoms 76
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction HKL-3000 data reduction HKL-3000 data scaling MOLREP phasing