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Crystal structure of a Cysteine Desulfurase from Thermococcus onnurineus NA1 in complex with alanine at 1.5 Angstrom resolution
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, SITTING DROP 289 0.03M NaNO3, 0.03M Na2HPO4 , 0.03M (NH4)2SO4, 20% (v/v) ethylene glycol, 15% (w/v) PEG 8000, 0.1M Imidazol/MES pH 6.5
Crystal Properties Matthews coefficient Solvent content 2.28 46.04
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 62.939 α = 90 b = 78.718 β = 90 c = 171.908 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 2014-07-11 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 1.5 50 94.1 0.089 62.9 12.5 128618
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 1.53 91.9 0.566 6.5 12.4
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 1.5 49.16 122068 6444 94.06 0.16806 0.1667 0.1706 0.19424 0.196 RANDOM 20.348
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_dihedral_angle_2_deg 33.129 r_dihedral_angle_4_deg 20.18 r_dihedral_angle_3_deg 12.757 r_long_range_B_refined 6.482 r_long_range_B_other 6.383 r_dihedral_angle_1_deg 6.024 r_scangle_other 5.268 r_scbond_it 3.591 r_scbond_other 3.589 r_angle_refined_deg 2.458
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.129 r_dihedral_angle_4_deg 20.18 r_dihedral_angle_3_deg 12.757 r_long_range_B_refined 6.482 r_long_range_B_other 6.383 r_dihedral_angle_1_deg 6.024 r_scangle_other 5.268 r_scbond_it 3.591 r_scbond_other 3.589 r_angle_refined_deg 2.458 r_mcangle_other 2.435 r_mcangle_it 2.434 r_mcbond_it 1.836 r_mcbond_other 1.832 r_angle_other_deg 1.178 r_chiral_restr 0.16 r_bond_refined_d 0.027 r_gen_planes_refined 0.014 r_bond_other_d 0.003 r_gen_planes_other 0.003 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 6256 Nucleic Acid Atoms Solvent Atoms 545 Heterogen Atoms 52
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing