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Crystal structure of dUTPase in complex with substrate analogue dUDP and manganese
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1EUW
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.8 293 20% PEG 3350, 0.2M SODIUM ACETATE, 0.1M TRIS, pH 7.8, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.49 50.61
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 75.049 α = 90 b = 75.049 β = 90 c = 99.936 γ = 120
Symmetry Space Group P 63 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 MAR CCD 165 mm mirror 2002-03-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE X11 0.8110 EMBL/DESY, HAMBURG X11
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 1.84 24.9 98 0.064 10.8 12.6 14703 14703 -3 22.35
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 1.84 1.89 98 0.558 1.3 10.1 815
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 (All) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1EUW 1.84 24.9 13953 13953 749 98.1 0.15168 0.15168 0.15054 0.17338 0.1763 RANDOM 22.763
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] -0.09 -0.04 -0.09 0.13
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.32 r_dihedral_angle_4_deg 16.193 r_dihedral_angle_3_deg 12.121 r_scangle_it 7.993 r_scbond_it 6.01 r_dihedral_angle_1_deg 5.818 r_mcangle_it 3.606 r_mcbond_it 2.23 r_angle_refined_deg 1.702 r_angle_other_deg 0.821
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.32 r_dihedral_angle_4_deg 16.193 r_dihedral_angle_3_deg 12.121 r_scangle_it 7.993 r_scbond_it 6.01 r_dihedral_angle_1_deg 5.818 r_mcangle_it 3.606 r_mcbond_it 2.23 r_angle_refined_deg 1.702 r_angle_other_deg 0.821 r_symmetry_hbond_refined 0.284 r_symmetry_vdw_other 0.251 r_nbd_refined 0.215 r_xyhbond_nbd_refined 0.203 r_nbd_other 0.191 r_symmetry_vdw_refined 0.171 r_nbtor_refined 0.164 r_chiral_restr 0.098 r_mcbond_other 0.093 r_nbtor_other 0.082 r_bond_refined_d 0.016 r_gen_planes_refined 0.007 r_bond_other_d 0.002 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1013 Nucleic Acid Atoms Solvent Atoms 156 Heterogen Atoms 29
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling MOLREP phasing