☰ Navigation Tabs
X-ray structure of Dps from Thermosynechococcus elongatus
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1JI4 PDB ENTRY 1JI4
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 5 0.1 M SODIUM ACETATE AT PH VALUES 4.0 AND 5.0, PEG4000 5-15 %
Crystal Properties Matthews coefficient Solvent content 2.08 40.27
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 122.972 α = 90 b = 122.887 β = 90 c = 253.305 γ = 90
Symmetry Space Group C 2 2 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 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ELETTRA BEAMLINE 5.2R ELETTRA 5.2R
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 1.8 30 97.7 0.05 8.3 174107
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.8 1.86 99 7.7
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 1JI4 1.81 30 161382 8507 97.3 0.169 0.168 0.1681 0.195 0.195 RANDOM 17.18
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] 0.25 -0.26 0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.134 r_dihedral_angle_4_deg 15.484 r_dihedral_angle_3_deg 14.257 r_dihedral_angle_1_deg 4.258 r_scangle_it 2.307 r_scbond_it 1.462 r_angle_refined_deg 1.064 r_mcangle_it 0.713 r_mcbond_it 0.499 r_nbtor_refined 0.301
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.134 r_dihedral_angle_4_deg 15.484 r_dihedral_angle_3_deg 14.257 r_dihedral_angle_1_deg 4.258 r_scangle_it 2.307 r_scbond_it 1.462 r_angle_refined_deg 1.064 r_mcangle_it 0.713 r_mcbond_it 0.499 r_nbtor_refined 0.301 r_symmetry_vdw_refined 0.241 r_symmetry_hbond_refined 0.216 r_nbd_refined 0.193 r_xyhbond_nbd_refined 0.125 r_chiral_restr 0.078 r_bond_refined_d 0.009 r_gen_planes_refined 0.004 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_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 14814 Nucleic Acid Atoms Solvent Atoms 1503 Heterogen Atoms 150
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling MOLREP phasing