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The crystal of rhodanese domain of YgaP treated with sodium thiosulfate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5HBO
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 295 0.2 M sodium acetate in 0.1 M Tris HCl pH 8.5, and 30% PEG 4000
Crystal Properties Matthews coefficient Solvent content 2.05 39.91
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 43.699 α = 90 b = 43.699 β = 90 c = 52.28 γ = 120
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 2013-03-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL12-2 1.127 SSRL BL12-2
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 1.66 37.84 98.4 0.037 34.4 5.3 13126
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 1.66 1.75 89.3 0.057 16.2 4.2
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 5HBO 1.66 37.84 12460 645 99.73 0.16845 0.16708 0.1789 0.1974 0.2081 RANDOM 16.007
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 0.01 0.01 -0.04
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.118 r_dihedral_angle_4_deg 17.197 r_dihedral_angle_3_deg 13.35 r_long_range_B_refined 5.537 r_long_range_B_other 5.169 r_dihedral_angle_1_deg 5.076 r_scangle_other 1.914 r_mcangle_it 1.631 r_mcangle_other 1.63 r_angle_refined_deg 1.619
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.118 r_dihedral_angle_4_deg 17.197 r_dihedral_angle_3_deg 13.35 r_long_range_B_refined 5.537 r_long_range_B_other 5.169 r_dihedral_angle_1_deg 5.076 r_scangle_other 1.914 r_mcangle_it 1.631 r_mcangle_other 1.63 r_angle_refined_deg 1.619 r_scbond_it 1.194 r_scbond_other 1.193 r_angle_other_deg 0.959 r_mcbond_it 0.945 r_mcbond_other 0.939 r_chiral_restr 0.076 r_bond_refined_d 0.009 r_gen_planes_refined 0.005 r_bond_other_d 0.003 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 794 Nucleic Acid Atoms Solvent Atoms 147 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling MOLREP phasing