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DIHYDROPYRIMIDINE DEHYDROGENASE (DPD) FROM PIG, BINARY COMPLEX WITH 5-IODOURACIL
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details other DIHYDROPYRIMIDINE DEHYDROGENASE, NON-LIGANDED FORM
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 4.7 100 MM SODIUM CITRATE PH 4.7, 16-20 % POLYETHYLENE GLYCOL 6000, 1 MM DTT, 1 MM 5-IODOURACIL
Crystal Properties Matthews coefficient Solvent content 2.35 38.4
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 81.71 α = 90 b = 158.37 β = 95.84 c = 162.33 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 IMAGE PLATE MARRESEARCH 2000-02-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE BW7B EMBL/DESY, HAMBURG BW7B
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 1.65 30 98.1 0.047 15 3.2 489160 17.3
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 1.65 1.74 94.3 0.238 4.3 2.7
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, NON-LIGANDED FORM 1.65 24.98 481625 9508 98 0.181 0.181 0.1778 0.197 0.1933 RANDOM 23
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] -4.46 -2.03 4.08 0.38
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 22.8 c_improper_angle_d 3.12 c_angle_deg 1.4 c_bond_d 0.009 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 22.8 c_improper_angle_d 3.12 c_angle_deg 1.4 c_bond_d 0.009 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 30790 Nucleic Acid Atoms Solvent Atoms 4848 Heterogen Atoms 500
Software Software Software Name Purpose CNS refinement DENZO data reduction SCALA data scaling AMoRE phasing