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Apo Structure of Cysteine Desulfurase from Thermococcus onnurineus NA1 at 1.89A
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5B7S
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 289 1mM PLP, 5mM cystine, 10% (v/v) Isopropanol, 5% (w/v) PEG 8000, Imidazol/HCl pH 5.9
Crystal Properties Matthews coefficient Solvent content 2.32 47
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 78.488 α = 90 b = 62.789 β = 90 c = 171.317 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 QUANTUM 315r 2015-03-31 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PAL/PLS BEAMLINE 5C (4A) 0.97 PAL/PLS 5C (4A)
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 1.9 50 97 0.062 54.02 9.6 66011
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 1.9 1.93 91.9 0.306 9 9.6
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 5B7S 1.9 46.177 62613 3326 96.95 0.16751 0.1656 0.1716 0.20309 0.2035 RANDOM 23.938
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] 0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.865 r_dihedral_angle_4_deg 17.662 r_dihedral_angle_3_deg 14.647 r_dihedral_angle_1_deg 6.232 r_long_range_B_refined 6.149 r_long_range_B_other 6.093 r_scangle_other 5.069 r_scbond_it 3.362 r_scbond_other 3.362 r_mcangle_it 2.635
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.865 r_dihedral_angle_4_deg 17.662 r_dihedral_angle_3_deg 14.647 r_dihedral_angle_1_deg 6.232 r_long_range_B_refined 6.149 r_long_range_B_other 6.093 r_scangle_other 5.069 r_scbond_it 3.362 r_scbond_other 3.362 r_mcangle_it 2.635 r_mcangle_other 2.635 r_mcbond_it 2.046 r_mcbond_other 2.04 r_angle_refined_deg 1.896 r_angle_other_deg 1.078 r_chiral_restr 0.132 r_bond_refined_d 0.02 r_gen_planes_refined 0.01 r_bond_other_d 0.002 r_gen_planes_other 0.002 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 6286 Nucleic Acid Atoms Solvent Atoms 259 Heterogen Atoms 11
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing