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Structural Analysis of Pneumocystis carinii and Human DHFR Complexes with NADPH and a Series of Five Potent 5-(omega-Carboxy(alkyloxy)Pyrido[2,3-d]pyrimidine Derivatives
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3CD2 PDB entry 3cd2
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6 273 33-336% PEG 2K, 46-52 mM MES pH 6 100 mM KCl, VAPOR DIFFUSION, HANGING DROP, temperature 273K
Crystal Properties Matthews coefficient Solvent content 1.97 37.69
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 36.952 α = 90 b = 42.673 β = 94.8 c = 60.099 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 200 CCD MARMOSAIC 325 mm CCD mirrors 2006-06-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL11-1 0.975 SSRL BL11-1
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 1.6 50 96.6 0.028 0.042 5 3.6 24011 22779 2 2 27.9
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) 1.6 1.66 90.3 0.33 0.113 13.1 3.2 2229
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 PDB entry 3cd2 1.8 24.51 2 2 24011 16107 886 97.15 0.20548 0.20181 0.2022 0.27184 0.2735 RANDOM 28.375
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 -0.01 0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.737 r_dihedral_angle_4_deg 17.939 r_dihedral_angle_3_deg 16.712 r_dihedral_angle_1_deg 6.993 r_scangle_it 4.847 r_scbond_it 3.267 r_mcangle_it 2.342 r_angle_refined_deg 2.336 r_mcbond_it 1.39 r_chiral_restr 0.174
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.737 r_dihedral_angle_4_deg 17.939 r_dihedral_angle_3_deg 16.712 r_dihedral_angle_1_deg 6.993 r_scangle_it 4.847 r_scbond_it 3.267 r_mcangle_it 2.342 r_angle_refined_deg 2.336 r_mcbond_it 1.39 r_chiral_restr 0.174 r_bond_refined_d 0.023 r_gen_planes_refined 0.011
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1686 Nucleic Acid Atoms Solvent Atoms 114 Heterogen Atoms 79
Software Software Software Name Purpose HKL-2000 data collection MOLREP phasing REFMAC refinement HKL-2000 data reduction SCALA data scaling