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High-resolution structure of a plasmid-encoded dihydrofolate reductase: pentagonal network of water molecules in the D2-symmetric active site
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1VIE PDB ENTRY 1VIE
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 277 0.1M Tris-Hcl buffer, 25% MPD, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.24 45.2
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 68.05 α = 90 b = 68.05 β = 90 c = 52.244 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 ADSC QUANTUM 1 1998-03-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 14-BM-D 0.9495 APS 14-BM-D
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.1 50 90 0.042 21.4 8.5 22453 19914 2 4 9.7
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1.1 1.14 58 0.34
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 1VIE 1.1 10 22389 19914 1121 86 0.105 0.099 0.1104 0.153 0.1315 RANDOM
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 s_non_zero_chiral_vol 0.175 s_zero_chiral_vol 0.118 s_approx_iso_adps 0.103 s_anti_bump_dis_restr 0.068 s_angle_d 0.035 s_similar_dist 0.034 s_similar_adp_cmpnt 0.034 s_from_restr_planes 0.0284 s_bond_d 0.023 s_rigid_bond_adp_cmpnt 0.012
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 455 Nucleic Acid Atoms Solvent Atoms 191 Heterogen Atoms
Software Software Software Name Purpose SHELXL-97 refinement DENZO data reduction CNS refinement ADSC data collection SCALEPACK data scaling CNS phasing