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Crystal structure of the ternary MTX NADPH complex of Escherichia coli dihydrofolate reductase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1RH3 PDB entry 1RH3
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.5 277 0.1 M Bis-Tris pH 5.5, 0.2 M NaCl, 25% w/v PEG 3350, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 3.21 61.67
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 61.847 α = 90 b = 61.847 β = 90 c = 104.74 γ = 120
Symmetry Space Group P 32 2 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD ADSC QUANTUM 315 Bent conical mirror 2005-03-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 14-BM-C 0.90000 APS 14-BM-C
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 1.35 20 98.6 0.059 16.7 5.5 55916 50833 1 1
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.35 1.4 98.4 0.921 1.24 2.9 5001
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 1RH3 1.5 18.88 1 1 37199 35313 1886 98.45 0.16 0.159 0.1654 0.186 0.1939 RANDOM 26.06
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] 0.1 0.05 0.1 -0.15
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.601 r_dihedral_angle_4_deg 14.319 r_sphericity_free 13.658 r_dihedral_angle_3_deg 13.389 r_sphericity_bonded 9.78 r_dihedral_angle_1_deg 5.846 r_scangle_it 5.287 r_scbond_it 4.1 r_mcangle_it 2.992 r_rigid_bond_restr 2.513
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.601 r_dihedral_angle_4_deg 14.319 r_sphericity_free 13.658 r_dihedral_angle_3_deg 13.389 r_sphericity_bonded 9.78 r_dihedral_angle_1_deg 5.846 r_scangle_it 5.287 r_scbond_it 4.1 r_mcangle_it 2.992 r_rigid_bond_restr 2.513 r_angle_refined_deg 2.219 r_mcbond_it 2.212 r_symmetry_vdw_refined 0.388 r_nbtor_refined 0.31 r_nbd_refined 0.207 r_symmetry_hbond_refined 0.174 r_chiral_restr 0.144 r_xyhbond_nbd_refined 0.112 r_bond_refined_d 0.022 r_gen_planes_refined 0.012
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1246 Nucleic Acid Atoms Solvent Atoms 159 Heterogen Atoms 81
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction BioCARS data collection HKL-2000 data reduction HKL-2000 data scaling PHASER phasing