☰ Navigation Tabs
DIHYDROPYRIMIDINE DEHYDROGENASE (DPD) FROM PIG, TERNARY COMPLEX WITH NADPH AND 5-IODOURACIL
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details other DIHYDROPYRIMIDINE DEHYDROGENASE, UNCOMPLEXED
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, 5 MM 5-IODOURACIL, 5 MM NADPH
Crystal Properties Matthews coefficient Solvent content 2.46 41
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 82.21 α = 90 b = 159.69 β = 97.11 c = 167.59 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 2000-10-09 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 2.25 30 98.3 0.064 14.3 3.6 200114 27.5
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 2.25 2.37 97.4 0.25 5.2 3.4
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, UNCOMPLEXED 2.25 25 199143 3984 98.1 0.177 0.177 0.1747 0.209 0.2048 RANDOM 33.3
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] -8.16 0.91 9.51 -1.35
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 22.9 c_improper_angle_d 3.11 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 22.9 c_improper_angle_d 3.11 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 30999 Nucleic Acid Atoms Solvent Atoms 3073 Heterogen Atoms 690
Software Software Software Name Purpose CNS refinement DENZO data reduction SCALA data scaling AMoRE phasing