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Structural Analysis of Pneumocystis carinii Dihydrofolate Reductase Complex with NADPH and 2,4-diamino-5-methyl-6-[2'-(4-carboxy-1-pentynyl)-5'-methoxybenzyl]pyrido[2,3-d]pyrimidine
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% PEG 2K, 46 mM MES, pH 6.0, 100 mM KCl, VAPOR DIFFUSION, HANGING DROP, temperature 273K
Crystal Properties Matthews coefficient Solvent content 1.92 35.94
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 36.123 α = 90 b = 42.63 β = 95.2 c = 59.894 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 113 CCD MARMOSAIC 325 mm CCD mirrors 2011-04-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL9-2 0.975 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 1.8 59.7 95.9 0.07 0.04 10.7 3.4 16268 15433 2 2
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) 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 35.97 16268 15433 823 95.56 0.20001 0.19684 0.1986 0.25916 0.2581 RANDOM 38.153
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 30.993 r_dihedral_angle_3_deg 19.444 r_dihedral_angle_4_deg 18.047 r_dihedral_angle_1_deg 7.307 r_scangle_it 4.974 r_scbond_it 3.383 r_mcangle_it 2.43 r_angle_refined_deg 2.334 r_mcbond_it 1.411 r_chiral_restr 0.174
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.993 r_dihedral_angle_3_deg 19.444 r_dihedral_angle_4_deg 18.047 r_dihedral_angle_1_deg 7.307 r_scangle_it 4.974 r_scbond_it 3.383 r_mcangle_it 2.43 r_angle_refined_deg 2.334 r_mcbond_it 1.411 r_chiral_restr 0.174 r_bond_refined_d 0.019 r_gen_planes_refined 0.011 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1597 Nucleic Acid Atoms Solvent Atoms 41 Heterogen Atoms 78
Software Software Software Name Purpose HKL-2000 data collection MOLREP phasing REFMAC refinement DENZO data reduction SCALA data scaling