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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 33-36% PEG 2K, 46-52 mM MES pH 6.0, 100 mM KCl, VAPOR DIFFUSION, HANGING DROP, temperature 273K
Crystal Properties Matthews coefficient Solvent content 1.99 38.26
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 36.959 α = 90 b = 42.679 β = 94.57 c = 60.609 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 1.7 60.5 97.5 0.07 0.064 4.4 2.5 21070 19446 2 2 29.7
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) 1.7 1.76 98 0.376 0.325 14.1 2 1144
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 1.9 27.89 2 2 21070 13884 749 97.35 0.21001 0.20592 0.2063 0.28178 0.2811 RANDOM 28.354
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 30.431 r_dihedral_angle_3_deg 18.034 r_dihedral_angle_4_deg 16.016 r_dihedral_angle_1_deg 8.578 r_scangle_it 4.767 r_scbond_it 3.076 r_angle_refined_deg 2.299 r_mcangle_it 2.236 r_mcbond_it 1.323 r_chiral_restr 0.16
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.431 r_dihedral_angle_3_deg 18.034 r_dihedral_angle_4_deg 16.016 r_dihedral_angle_1_deg 8.578 r_scangle_it 4.767 r_scbond_it 3.076 r_angle_refined_deg 2.299 r_mcangle_it 2.236 r_mcbond_it 1.323 r_chiral_restr 0.16 r_bond_refined_d 0.022 r_gen_planes_refined 0.01
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1686 Nucleic Acid Atoms Solvent Atoms 117 Heterogen Atoms 80
Software Software Software Name Purpose HKL-2000 data collection MOLREP phasing REFMAC refinement HKL-2000 data reduction SCALA data scaling