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Electrostatics of Active Site Microenvironments of E. coli DHFR
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4GH8
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 293 100 mM Calcium Acetate
34% PEG 400
100 mM HEPES
Crystal Properties Matthews coefficient Solvent content 2.11 41.72
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 34.411 α = 90 b = 44.861 β = 90 c = 98.428 γ = 90
Symmetry Space Group P 21 21 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 210 2013-07-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON CHESS BEAMLINE A1 0.978 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 1.83 50 97.3 0.107 16.7 3.9 13385
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 1.83 1.86 93.8 0.311 3.5 640
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 4GH8 1.84 49.21 13352 668 96.72 0.1901 0.1881 0.1975 0.2293 0.2345 RANDOM 17.67
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] -0.41 1.02 -0.61
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.705 r_dihedral_angle_3_deg 13.479 r_dihedral_angle_4_deg 10.051 r_dihedral_angle_1_deg 5.617 r_scangle_it 3.632 r_scbond_it 2.302 r_mcangle_it 1.67 r_angle_refined_deg 1.531 r_angle_other_deg 1.084 r_mcbond_it 0.884
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.705 r_dihedral_angle_3_deg 13.479 r_dihedral_angle_4_deg 10.051 r_dihedral_angle_1_deg 5.617 r_scangle_it 3.632 r_scbond_it 2.302 r_mcangle_it 1.67 r_angle_refined_deg 1.531 r_angle_other_deg 1.084 r_mcbond_it 0.884 r_mcbond_other 0.214 r_chiral_restr 0.093 r_bond_refined_d 0.014 r_bond_other_d 0.006 r_gen_planes_refined 0.006 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1239 Nucleic Acid Atoms Solvent Atoms 88 Heterogen Atoms 83
Software Software Software Name Purpose HKL-2000 data reduction REFMAC refinement PDB_EXTRACT data extraction