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HUMAN DIHYDROFOLATE REDUCTASE COMPLEXED WITH NADPH AND FOLATE
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1DRF PDB ENTRY 1DRF
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.75 277 HUMAN DHFR/FOLATE COMPLEX WAS MIXED WITH NADPH (2 MM FINAL). CRYSTALS WERE GROWN BY HANGING DROP VAPOR DIFFUSION AT 277 K BY MIXING EQUAL VOLUMES OF PROTEIN/NADPH/FOLATE WITH RESERVOIR (24% PEG 4000, 200 MM LI2SO4, 100 MM TRIS.HCL, PH 8.75). TRUNCATED TRIANGULAR CRYSTALS APPEARED SLOWLY, IN ABOUT A MONTH. THE CRYSTAL WAS CRYOPROTECTED WITH 15% GLYCEROL AND FLASH-COOLED IN LIQUID N2.
Crystal Properties Matthews coefficient Solvent content 2.35 47.72
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 88.552 α = 90 b = 94.269 β = 90 c = 96.681 γ = 90
Symmetry Space Group C 2 2 21
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-1 MIRRORS 1996-06-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON CHESS BEAMLINE A1 CHESS A1
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 1.6 10.7 98.4 0.05 4.5 5.6 52618 -10 19.9
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 1.6 1.69 93.6 0.35 1.8 3.1
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) 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 1DRF 1.6 10.7 49931 2660 98.1 0.169 0.167 0.2193 0.208 0.2565 RANDOM 14.09
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 0.05 -0.06
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.505 r_dihedral_angle_4_deg 11.845 r_dihedral_angle_3_deg 11.565 r_dihedral_angle_1_deg 5.917 r_scangle_it 3.148 r_scbond_it 2.47 r_mcangle_it 1.592 r_angle_refined_deg 1.583 r_mcbond_it 1.343 r_angle_other_deg 1.233
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.505 r_dihedral_angle_4_deg 11.845 r_dihedral_angle_3_deg 11.565 r_dihedral_angle_1_deg 5.917 r_scangle_it 3.148 r_scbond_it 2.47 r_mcangle_it 1.592 r_angle_refined_deg 1.583 r_mcbond_it 1.343 r_angle_other_deg 1.233 r_symmetry_vdw_refined 0.256 r_nbd_refined 0.2 r_symmetry_vdw_other 0.196 r_nbd_other 0.19 r_symmetry_hbond_refined 0.179 r_nbtor_refined 0.174 r_xyhbond_nbd_refined 0.15 r_chiral_restr 0.096 r_nbtor_other 0.081 r_bond_refined_d 0.013 r_gen_planes_refined 0.007 r_gen_planes_other 0.002 r_bond_other_d 0.001 r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2946 Nucleic Acid Atoms Solvent Atoms 494 Heterogen Atoms 160
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling Agrovata data scaling AMoRE phasing