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Structure of Human cytosolic deoxyribonucleotidase in complex with deoxyuridine, AlF4 and Mg2+
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.5 298 50mM KH2PO4, 2-15% w/v PEG 8000, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.32 46.95
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 39.623 α = 68.92 b = 47.153 β = 81.69 c = 62.384 γ = 74.99
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 MAR CCD 165 mm 2003-09-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE X11 0.8133 EMBL/DESY, HAMBURG X11
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 1.2 19.12 93.1 0.067 0.068 10.24 3.5 120303 120303 13.959
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1.2 1.3 86.8 0.357 0.31 3.2 23589
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 1.2 19.1 118444 118444 6001 94.67 0.167 0.166 0.166 0.1669 0.196 0.1978 RANDOM 13.221
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] 0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.468 r_dihedral_angle_4_deg 16.413 r_dihedral_angle_3_deg 12.365 r_dihedral_angle_1_deg 5.649 r_scangle_it 3.174 r_sphericity_free 3.128 r_sphericity_bonded 2.553 r_scbond_it 2.538 r_rigid_bond_restr 1.914 r_mcangle_it 1.614
Show All KeysRMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.468 r_dihedral_angle_4_deg 16.413 r_dihedral_angle_3_deg 12.365 r_dihedral_angle_1_deg 5.649 r_scangle_it 3.174 r_sphericity_free 3.128 r_sphericity_bonded 2.553 r_scbond_it 2.538 r_rigid_bond_restr 1.914 r_mcangle_it 1.614 r_angle_refined_deg 1.463 r_mcbond_it 1.148 r_nbtor_refined 0.292 r_nbd_refined 0.202 r_symmetry_vdw_refined 0.155 r_xyhbond_nbd_refined 0.14 r_chiral_restr 0.096 r_symmetry_hbond_refined 0.091 r_bond_refined_d 0.015 r_gen_planes_refined 0.006
Hide All KeysNon-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3173 Nucleic Acid Atoms Solvent Atoms 692 Heterogen Atoms 44
Software Software Software Name Purpose XSCALE data scaling REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data collection XDS data reduction CNS phasing