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Apo structure of Cysteine Desulfurase from Thermococcus onnurineus NA1
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1T3I
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 287 0.03M MgCl2, 0.03 M CaCl2, 15% (v/v) glycerol, 15% (w/v) PEG 4000, 0.1M Tris (base)/ Bicine pH 8.5
Crystal Properties Matthews coefficient Solvent content 2.58 52.33
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 67.006 α = 90 b = 92.527 β = 90 c = 145.444 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 270 2014-06-11 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PAL/PLS BEAMLINE 7A (6B, 6C1) 0.979 PAL/PLS 7A (6B, 6C1)
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 2.58 50 99.9 0.119 29.1 6.8 28968
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 2.6 2.64 100 0.413 7.1 7.1
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1T3I 2.58 36.36 27449 1465 99.16 0.2078 0.2032 0.2951 0.2865 RANDOM 52.856
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] 0.02 -0.03 0.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.422 r_dihedral_angle_3_deg 21.485 r_dihedral_angle_4_deg 15.371 r_dihedral_angle_1_deg 7.844 r_mcangle_it 5.171 r_mcbond_it 3.375 r_mcbond_other 3.374 r_angle_refined_deg 1.81 r_angle_other_deg 1.167 r_chiral_restr 0.123
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.422 r_dihedral_angle_3_deg 21.485 r_dihedral_angle_4_deg 15.371 r_dihedral_angle_1_deg 7.844 r_mcangle_it 5.171 r_mcbond_it 3.375 r_mcbond_other 3.374 r_angle_refined_deg 1.81 r_angle_other_deg 1.167 r_chiral_restr 0.123 r_bond_refined_d 0.013 r_gen_planes_refined 0.007 r_bond_other_d 0.003 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6152 Nucleic Acid Atoms Solvent Atoms 101 Heterogen Atoms 12
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction DENZO data reduction DENZO data scaling MOLREP phasing