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Correlations of Inhibitor Kinetics for Pneumocystis jirovecii and Human Dihydrofolate Reductase with Structural Data for Human Active Site Mutant Enzyme Complexes
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 6.9 287 100 mM K2PO4, pH 6.9, 60% sat. AS with 3% ethanol, VAPOR DIFFUSION, HANGING DROP, temperature 287K
Crystal Properties Matthews coefficient Solvent content 2.49 50.56
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 84.098 α = 90 b = 84.098 β = 90 c = 78.054 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 IMAGE PLATE MAR scanner 300 mm plate mirrors 2008-12-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL9-2 1.000 SSRL BL9-2
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 1.23 53.2 100 0.07 0.02 20.8 11.1 59797 56766 2 2 30
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 1.23 1.33 100 0.4 0.324 2.5 10.7 939
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (I) Cut-off Sigma (F) Number Reflections (All) 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 1u72 1.23 34.4 2 2 59797 56758 3022 99.98 0.24572 0.24494 0.2407 0.26019 0.2559 RANDOM 16.036
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.437 r_dihedral_angle_3_deg 14.932 r_dihedral_angle_4_deg 10.923 r_dihedral_angle_1_deg 5.759 r_scangle_it 2.724 r_scbond_it 1.954 r_angle_refined_deg 1.577 r_mcangle_it 1.307 r_mcbond_it 0.861 r_nbtor_refined 0.309
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.437 r_dihedral_angle_3_deg 14.932 r_dihedral_angle_4_deg 10.923 r_dihedral_angle_1_deg 5.759 r_scangle_it 2.724 r_scbond_it 1.954 r_angle_refined_deg 1.577 r_mcangle_it 1.307 r_mcbond_it 0.861 r_nbtor_refined 0.309 r_nbd_refined 0.198 r_symmetry_vdw_refined 0.176 r_chiral_restr 0.126 r_xyhbond_nbd_refined 0.126 r_symmetry_hbond_refined 0.086 r_bond_refined_d 0.009 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1502 Nucleic Acid Atoms Solvent Atoms 67 Heterogen Atoms 73
Software Software Software Name Purpose HKL-2000 data collection MOLREP phasing REFMAC refinement MOSFLM data reduction SCALA data scaling