☰ Navigation Tabs
Sulfur Oxygenase Reductase from Thioalkalivibrio paradoxus
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6QPA
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 295 0.9 M sodium acetate and 0.1 M sodium cacodylate, pH 6.5
Crystal Properties Matthews coefficient Solvent content 2.98 58.69
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 278.028 α = 90 b = 278.028 β = 90 c = 278.028 γ = 90
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 EIGER2 X 9M 2017-12-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID30B 1.7373 ESRF ID30B
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.85 80.26 99.9 0.311 0.0727 0.99 13.99 17.9 162113 76.64
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.85 3.01 99.9 0.081 0.082 0.293 0.315 0.87
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2.85 80.26 83499 4125 99.929 0.166 0.1627 0.1907 0.2228 0.219 58.898
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_lrange_it 33.801 r_scangle_it 19.803 r_mcangle_it 17.453 r_dihedral_angle_3_deg 15.828 r_dihedral_angle_6_deg 14.674 r_scbond_it 13.002 r_mcbond_it 10.931 r_dihedral_angle_2_deg 6.914 r_dihedral_angle_1_deg 5.936 r_rigid_bond_restr 3.598
RMS Deviations Key Refinement Restraint Deviation r_lrange_it 33.801 r_scangle_it 19.803 r_mcangle_it 17.453 r_dihedral_angle_3_deg 15.828 r_dihedral_angle_6_deg 14.674 r_scbond_it 13.002 r_mcbond_it 10.931 r_dihedral_angle_2_deg 6.914 r_dihedral_angle_1_deg 5.936 r_rigid_bond_restr 3.598 r_angle_refined_deg 1.907 r_symmetry_xyhbond_nbd_refined 0.321 r_symmetry_nbd_refined 0.313 r_nbtor_refined 0.312 r_nbd_refined 0.242 r_xyhbond_nbd_refined 0.174 r_chiral_restr 0.126 r_ncsr_local_group_14 0.105 r_ncsr_local_group_17 0.105 r_ncsr_local_group_21 0.104 r_ncsr_local_group_8 0.099 r_ncsr_local_group_9 0.099 r_ncsr_local_group_12 0.098 r_ncsr_local_group_19 0.098 r_ncsr_local_group_22 0.097 r_ncsr_local_group_28 0.097 r_ncsr_local_group_3 0.096 r_ncsr_local_group_24 0.095 r_ncsr_local_group_6 0.093 r_ncsr_local_group_20 0.093 r_ncsr_local_group_11 0.092 r_ncsr_local_group_2 0.091 r_ncsr_local_group_26 0.09 r_ncsr_local_group_10 0.089 r_ncsr_local_group_16 0.089 r_ncsr_local_group_15 0.088 r_ncsr_local_group_13 0.087 r_ncsr_local_group_1 0.086 r_ncsr_local_group_7 0.086 r_ncsr_local_group_18 0.085 r_ncsr_local_group_4 0.083 r_ncsr_local_group_25 0.082 r_ncsr_local_group_23 0.078 r_ncsr_local_group_5 0.077 r_ncsr_local_group_27 0.077 r_bond_refined_d 0.01 r_gen_planes_refined 0.007 r_ext_dist_refined_b
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 19397 Nucleic Acid Atoms Solvent Atoms 21 Heterogen Atoms 36
Software Software Software Name Purpose XDS data reduction XDS data scaling MoRDa phasing PHENIX refinement