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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]pyridine Derivativea
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 30-36% PEG 2K, 46-52 mM MES, 100 mM KCl, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 273K
Crystal Properties Matthews coefficient Solvent content 1.96 37.36
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 36.859 α = 90 b = 42.667 β = 94.77 c = 59.936 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 1.8 50 95.8 0.06 0.065 0.073 4.9 17462 16731 2 2 31.1
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) 1.8 1.86 83.8 0.34 0.41 3.2 3.3 1469
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB entry 3cd2 2 32.51 2 2 17462 11845 636 98.03 0.21222 0.20949 0.26035 0.2917 RANDOM 39.197
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] 0.03 -0.07 0.04
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.629 r_dihedral_angle_4_deg 21.127 r_dihedral_angle_3_deg 19.205 r_dihedral_angle_1_deg 9.3 r_scangle_it 5.094 r_scbond_it 3.333 r_mcangle_it 2.462 r_angle_refined_deg 2.124 r_mcbond_it 1.418 r_chiral_restr 0.178
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.629 r_dihedral_angle_4_deg 21.127 r_dihedral_angle_3_deg 19.205 r_dihedral_angle_1_deg 9.3 r_scangle_it 5.094 r_scbond_it 3.333 r_mcangle_it 2.462 r_angle_refined_deg 2.124 r_mcbond_it 1.418 r_chiral_restr 0.178 r_bond_refined_d 0.023 r_gen_planes_refined 0.01
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1686 Nucleic Acid Atoms Solvent Atoms 48 Heterogen Atoms 48
Software Software Software Name Purpose HKL-2000 data collection MOLREP phasing REFMAC refinement HKL-2000 data reduction SCALA data scaling