☰ Navigation Tabs
Twist and induce: Dissecting the link between the enzymatic activity and the SaPI inducing capacity of the phage 80 dUTPase. D95E mutant from dUTPase 80alpha phage.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3ZEZ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 4.2 296 32% Etanol, 2% PEG 1000, 0.1M phosphate citrate pH 4.2
Crystal Properties Matthews coefficient Solvent content 2.4 48.82
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 87.192 α = 90 b = 87.192 β = 90 c = 87.192 γ = 90
Symmetry Space Group P 21 3
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS PILATUS 6M-F 2013-07-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.97949 Diamond I04
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 2.85 38.99 96.1 0.102 5.2 2.2 5130
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 2.85 3 96.1 0.394 2.3
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 3ZEZ 2.85 38.99 4894 235 95.62 0.2307 0.22832 0.27753 0.2858 RANDOM 56.224
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.436 r_dihedral_angle_4_deg 21.198 r_dihedral_angle_3_deg 14.5 r_dihedral_angle_1_deg 5.642 r_long_range_B_refined 3.489 r_long_range_B_other 3.375 r_mcangle_it 1.831 r_mcangle_other 1.83 r_scangle_other 1.226 r_angle_refined_deg 1.04
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.436 r_dihedral_angle_4_deg 21.198 r_dihedral_angle_3_deg 14.5 r_dihedral_angle_1_deg 5.642 r_long_range_B_refined 3.489 r_long_range_B_other 3.375 r_mcangle_it 1.831 r_mcangle_other 1.83 r_scangle_other 1.226 r_angle_refined_deg 1.04 r_mcbond_it 1.005 r_mcbond_other 1.005 r_angle_other_deg 0.779 r_scbond_it 0.649 r_scbond_other 0.649 r_chiral_restr 0.062 r_bond_refined_d 0.006 r_gen_planes_refined 0.003 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1200 Nucleic Acid Atoms Solvent Atoms 21 Heterogen Atoms 29
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling PHASER phasing PHENIX refinement