☰ Navigation Tabs
Wild-type NIS synthetase DesD bound to AMP and substrate analog cadaverine
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2X0O PDB entry 2X0O
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 298 0.16 M magnesium chloride, 20% PEG, 0.08 M Tris hexahydrate, pH 8.5, 15% glycerol, 10% ethylene glycol
Crystal Properties Matthews coefficient Solvent content 2.51 50.9
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 98.43 α = 90 b = 74.24 β = 94.7 c = 183.17 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 80 IMAGE PLATE RIGAKU RAXIS HTC varimax DW 2014-04-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU R-AXIS IV 1.54180
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) 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 2.4 89.53 96.2 0.09 0.121 0.081 0.993 9.5 3.8 99262
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.4 2.44 94.3 0.344 0.456 0.296 0.841 3.5 3.9
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 (All) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB entry 2X0O 2.4 69.832 99234 4971 95.851 0.171 0.1681 0.2267 0.2208 RANDOM 22.251
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] 0.763 -0.357 -0.661 -0.042
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.525 r_dihedral_angle_4_deg 21.252 r_dihedral_angle_3_deg 16.28 r_dihedral_angle_1_deg 8.096 r_lrange_it 3.419 r_lrange_other 3.419 r_angle_other_deg 2.405 r_angle_refined_deg 1.846 r_mcangle_it 1.471 r_mcangle_other 1.471
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.525 r_dihedral_angle_4_deg 21.252 r_dihedral_angle_3_deg 16.28 r_dihedral_angle_1_deg 8.096 r_lrange_it 3.419 r_lrange_other 3.419 r_angle_other_deg 2.405 r_angle_refined_deg 1.846 r_mcangle_it 1.471 r_mcangle_other 1.471 r_scangle_it 1.388 r_scangle_other 1.388 r_mcbond_it 0.818 r_mcbond_other 0.818 r_scbond_it 0.813 r_scbond_other 0.813 r_symmetry_nbd_other 0.22 r_nbd_refined 0.21 r_nbd_other 0.21 r_xyhbond_nbd_refined 0.175 r_nbtor_refined 0.17 r_symmetry_xyhbond_nbd_refined 0.16 r_symmetry_nbd_refined 0.156 r_chiral_restr 0.086 r_symmetry_nbtor_other 0.073 r_symmetry_xyhbond_nbd_other 0.056 r_bond_other_d 0.035 r_metal_ion_refined 0.03 r_gen_planes_other 0.013 r_bond_refined_d 0.012 r_gen_planes_refined 0.009
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 18780 Nucleic Acid Atoms Solvent Atoms 937 Heterogen Atoms 120
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction CrystalClear data reduction CrystalClear data scaling PHASER phasing