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Structural, Computational and Kinetic Data for Antifolate Interactions Against Pneumocystis jirovecii, Pneumocystis carinii and Human Dihydrofolate Reductase and Their Active Site Mutants
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1U72
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.9 280 60-64% saturate ammonium sufate, 3% ethanol, pH 6.9, VAPOR DIFFUSION, HANGING DROP, temperature 280K
Crystal Properties Matthews coefficient Solvent content 2.53 51.3
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 84.53 α = 90 b = 84.53 β = 90 c = 78.423 γ = 120
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 200 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RU300 1.54118
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym I (Observed) 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 26.1 97.8 0.18 0.1 14.4 4.3 21070 13350 2 1 15
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2 2.1 99.9 0.9 0.011 4.6 4 2070
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (I) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 1U72 2 26.1 2 14132 12677 668 94.52 0.178 0.17461 0.17057 0.1703 0.25711 0.2556 RANDOM 22.161
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] -0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.362 r_dihedral_angle_4_deg 16.576 r_dihedral_angle_3_deg 16.557 r_dihedral_angle_1_deg 6.676 r_scangle_it 4.956 r_scbond_it 3.319 r_angle_refined_deg 2.342 r_mcangle_it 2.027 r_mcbond_it 1.183 r_chiral_restr 0.23
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.362 r_dihedral_angle_4_deg 16.576 r_dihedral_angle_3_deg 16.557 r_dihedral_angle_1_deg 6.676 r_scangle_it 4.956 r_scbond_it 3.319 r_angle_refined_deg 2.342 r_mcangle_it 2.027 r_mcbond_it 1.183 r_chiral_restr 0.23 r_bond_refined_d 0.025 r_gen_planes_refined 0.01
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1502 Nucleic Acid Atoms Solvent Atoms 189 Heterogen Atoms 75
Software Software Software Name Purpose CrystalClear data collection MOLREP phasing REFMAC refinement MOSFLM data reduction SCALA data scaling