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Crystal structure of DfrA1 dihydrofolate reductase in complex with TRIMETHOPRIM
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5ECC
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 277.15 22% PEG3350, 0.1M Na-Cacodylate pH 6.5, 0.36M MgCl2 and 2 mM DTT
Crystal Properties Matthews coefficient Solvent content 2.33 47.11
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 55.072 α = 90 b = 72.89 β = 90.56 c = 125.122 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 PIXEL DECTRIS EIGER X 9M 2020-11-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS-II BEAMLINE 17-ID-1 0.9201 NSLS-II 17-ID-1
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 2.15 72.89 98.6 0.19 0.206 0.078 0.993 7.6 6.8 53224 23.3
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 2.15 2.21 97.8 0.905 0.983 0.379 0.558 1.9 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 5ECC 2.15 63.06 50486 2718 98.34 0.2173 0.2147 0.2224 0.2659 0.2711 RANDOM 29.331
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] -0.6 -0.63 2.38 -1.76
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.538 r_dihedral_angle_4_deg 21.277 r_dihedral_angle_3_deg 18.029 r_dihedral_angle_1_deg 9.153 r_angle_refined_deg 1.414 r_angle_other_deg 1.15 r_chiral_restr 0.059 r_bond_refined_d 0.005 r_gen_planes_refined 0.005 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.538 r_dihedral_angle_4_deg 21.277 r_dihedral_angle_3_deg 18.029 r_dihedral_angle_1_deg 9.153 r_angle_refined_deg 1.414 r_angle_other_deg 1.15 r_chiral_restr 0.059 r_bond_refined_d 0.005 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7442 Nucleic Acid Atoms Solvent Atoms 49 Heterogen Atoms 126
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction Aimless data scaling PHASER phasing PDB_EXTRACT data extraction