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Crystal structure of DfrA5 dihydrofolate reductase in complex with TRIMETHOPRIM and NADPH
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1RX2
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6 277.15 23% to 25% PEG3350, 0.1M Mes pH 6.0, 0.3M LiSO4 and 2mM DTT
Crystal Properties Matthews coefficient Solvent content 3.02 59.3
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 99.53 α = 90 b = 99.53 β = 90 c = 42.82 γ = 90
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 2019-01-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X25 0.9795 NSLS X25
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 2.61 99.53 99.9 0.17 0.074 0.971 7.9 6.3 13057 35.09
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.61 2.73 100 0.497 0.591 2 6.5
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 1RX2 2.61 99.53 12280 742 99.63 0.18 0.1774 0.1813 0.224 0.2293 RANDOM 42.102
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] 0.81 0.81 -1.63
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.687 r_dihedral_angle_3_deg 18.593 r_dihedral_angle_4_deg 15.18 r_dihedral_angle_1_deg 9.401 r_angle_refined_deg 1.89 r_angle_other_deg 1.287 r_chiral_restr 0.073 r_bond_refined_d 0.012 r_gen_planes_refined 0.009 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.687 r_dihedral_angle_3_deg 18.593 r_dihedral_angle_4_deg 15.18 r_dihedral_angle_1_deg 9.401 r_angle_refined_deg 1.89 r_angle_other_deg 1.287 r_chiral_restr 0.073 r_bond_refined_d 0.012 r_gen_planes_refined 0.009 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2470 Nucleic Acid Atoms Solvent Atoms 12 Heterogen Atoms 126
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data reduction HKL-2000 data scaling PHASER phasing