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DHFR R67 Complexed with NADP and dihydrofolate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2RH2
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 8 277 50% 2-methyl-2,4-pentanediol (MPD), 100 mM Tris, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K, pH 8.00
Crystal Properties Matthews coefficient Solvent content 2.23 44.79
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 67.804 α = 90 b = 67.804 β = 90 c = 52.201 γ = 90
Symmetry Space Group I 41 2 2
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 RIGAKU SATURN 92 VARIMAX HF, CONFOCAL MIRRORS 2005-03-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 HF
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 1.26 50 99.6 0.072 14.1 12.4 15838 -3
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) 1.26 1.29 96.5 0.499 3 5.4
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2RH2 1.26 26.22 16692 15838 854 99.67 0.12419 0.12266 0.15231 0.1397 RANDOM, preserved from 2RH2 14.403
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 34.012 r_sphericity_free 20.897 r_dihedral_angle_3_deg 12.569 r_dihedral_angle_4_deg 11.459 r_sphericity_bonded 6.865 r_scangle_it 6.56 r_dihedral_angle_1_deg 6.219 r_scbond_it 4.852 r_mcangle_it 3.166 r_rigid_bond_restr 2.563
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.012 r_sphericity_free 20.897 r_dihedral_angle_3_deg 12.569 r_dihedral_angle_4_deg 11.459 r_sphericity_bonded 6.865 r_scangle_it 6.56 r_dihedral_angle_1_deg 6.219 r_scbond_it 4.852 r_mcangle_it 3.166 r_rigid_bond_restr 2.563 r_mcbond_it 2.499 r_angle_refined_deg 2.121 r_mcbond_other 1.359 r_angle_other_deg 0.87 r_symmetry_vdw_other 0.326 r_nbd_refined 0.298 r_xyhbond_nbd_refined 0.293 r_nbd_other 0.245 r_nbtor_refined 0.225 r_symmetry_vdw_refined 0.163 r_symmetry_hbond_refined 0.141 r_nbtor_other 0.106 r_chiral_restr 0.102 r_bond_refined_d 0.016 r_gen_planes_refined 0.009 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
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1034 Nucleic Acid Atoms Solvent Atoms 122 Heterogen Atoms 85
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling CNS phasing