☰ Navigation Tabs
Crystal structure of the T. thermophilus dodecin W38F mutant
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2V18 PDB ENTRY 2V18
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 0.2 M AMMONIUM ACETATE, 0.1 M SODIUM CITRATE, PH 5.2, 22.5 % MPD
Crystal Properties Matthews coefficient Solvent content 2.56 60
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 67.63 α = 90 b = 98.55 β = 90 c = 139.84 γ = 90
Symmetry Space Group P 21 21 21
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 ADSC CCD TOROIDAL MIRROR 2007-11-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-2 ESRF ID14-2
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 1.5 9.99 97.4 0.07 6.7 4.7 178447
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 1.5 1.54 96.5 0.37 2.1
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 PDB ENTRY 2V18 1.5 9.99 138426 7159 97.5 0.22 0.218 0.2259 0.25 0.2186 RANDOM 18.35
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] -0.76 -0.74 1.5
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 26.859 r_dihedral_angle_4_deg 17.946 r_dihedral_angle_3_deg 14.351 r_dihedral_angle_1_deg 5.85 r_scangle_it 3.058 r_scbond_it 1.763 r_angle_refined_deg 1.423 r_mcangle_it 1.367 r_angle_other_deg 0.889 r_mcbond_it 0.727
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 26.859 r_dihedral_angle_4_deg 17.946 r_dihedral_angle_3_deg 14.351 r_dihedral_angle_1_deg 5.85 r_scangle_it 3.058 r_scbond_it 1.763 r_angle_refined_deg 1.423 r_mcangle_it 1.367 r_angle_other_deg 0.889 r_mcbond_it 0.727 r_symmetry_hbond_refined 0.214 r_nbd_other 0.199 r_symmetry_vdw_other 0.189 r_nbtor_refined 0.178 r_nbd_refined 0.177 r_xyhbond_nbd_refined 0.142 r_symmetry_vdw_refined 0.117 r_nbtor_other 0.083 r_chiral_restr 0.073 r_bond_refined_d 0.009 r_gen_planes_refined 0.004 r_bond_other_d 0.002 r_gen_planes_other 0.001 r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6326 Nucleic Acid Atoms Solvent Atoms 532 Heterogen Atoms 953
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling MOLREP phasing