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The crystal of rhodanese domain of YgaP treated with SNOC
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5HBL
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 2.08 40.93
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 43.872 α = 90 b = 43.872 β = 90 c = 52.64 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 2013-05-29 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 1.5 38 93.9 0.082 18.7 4.9 16889
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 61.5 0.49 1.9 2.4
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 5HBL 1.5 37.99 15970 842 93.4 0.17244 0.17174 0.181 0.18474 0.1959 RANDOM 16.367
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 36.543 r_dihedral_angle_4_deg 14.893 r_dihedral_angle_3_deg 11.979 r_long_range_B_refined 5.234 r_dihedral_angle_1_deg 5.046 r_long_range_B_other 4.882 r_scangle_other 2.115 r_mcangle_it 1.497 r_mcangle_other 1.496 r_angle_refined_deg 1.446
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.543 r_dihedral_angle_4_deg 14.893 r_dihedral_angle_3_deg 11.979 r_long_range_B_refined 5.234 r_dihedral_angle_1_deg 5.046 r_long_range_B_other 4.882 r_scangle_other 2.115 r_mcangle_it 1.497 r_mcangle_other 1.496 r_angle_refined_deg 1.446 r_scbond_it 1.302 r_scbond_other 1.3 r_angle_other_deg 0.951 r_mcbond_it 0.886 r_mcbond_other 0.879 r_chiral_restr 0.078 r_bond_refined_d 0.009 r_gen_planes_refined 0.005 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 787 Nucleic Acid Atoms Solvent Atoms 147 Heterogen Atoms 3
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing