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DIHYDROPYRIMIDINE DEHYDROGENASE (DPD) FROM PIG, TERNARY COMPLEX WITH NADPH AND URACIL-4-ACETIC ACID
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details other DIHYDROPYRIMIDINE DEHYDROGENASE, TERNARY COMPLEX WITH 5-IODOURACIL AND NADPH, PH 7.5
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7.5 100 MM SODIUM CITRATE PH 4.7, 16-20% POLYETHYLENE GLYCOL 6000, 1 MM DTT
Crystal Properties Matthews coefficient Solvent content 2.45 40.03
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 82.03 α = 90 b = 159.53 β = 97.16 c = 166.02 γ = 90
Symmetry Space Group P 1 21 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 MARRESEARCH 2000-12-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-3 ESRF ID14-3
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 3.3 30 98.3 0.109 9.8 3.5 62722 28.1
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 3.3 3.36 92.9 0.463 2.6 3.2
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 DIHYDROPYRIMIDINE DEHYDROGENASE, TERNARY COMPLEX WITH 5-IODOURACIL AND NADPH, PH 7.5 3.3 29.75 62701 1247 98.4 0.214 0.214 0.1945 0.269 0.2421 RANDOM 53.3
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] -12.56 5.59 18.76 -6.21
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 22.9 c_improper_angle_d 3.12 c_angle_deg 1.5 c_bond_d 0.011 c_bond_d_na c_bond_d_prot c_angle_d c_angle_d_na c_angle_d_prot c_angle_deg_na
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 22.9 c_improper_angle_d 3.12 c_angle_deg 1.5 c_bond_d 0.011 c_bond_d_na c_bond_d_prot c_angle_d c_angle_d_na c_angle_d_prot c_angle_deg_na c_angle_deg_prot c_dihedral_angle_d_na c_dihedral_angle_d_prot c_improper_angle_d_na c_improper_angle_d_prot c_mcbond_it c_mcangle_it c_scbond_it c_scangle_it
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 30884 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 704
Software Software Software Name Purpose CNS refinement DENZO data reduction SCALA data scaling AMoRE phasing