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C63D mutant of the rhodanese domain of YgaP
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 40.97
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 43.896 α = 90 b = 43.896 β = 90 c = 52.667 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 2013-03-04 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 38 99.6 0.068 15.3 5.2 13404
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 98 0.67 2 4 1947
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 1.66 38 12627 658 98.85 0.18742 0.18572 0.2244 0.22252 0.2679 RANDOM 19.07
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] -2.49 -2.49 4.98
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.984 r_dihedral_angle_3_deg 13.806 r_dihedral_angle_4_deg 12.419 r_dihedral_angle_1_deg 5.879 r_long_range_B_refined 4.559 r_long_range_B_other 4.341 r_scangle_other 2.341 r_mcangle_it 1.673 r_mcangle_other 1.673 r_angle_refined_deg 1.579
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.984 r_dihedral_angle_3_deg 13.806 r_dihedral_angle_4_deg 12.419 r_dihedral_angle_1_deg 5.879 r_long_range_B_refined 4.559 r_long_range_B_other 4.341 r_scangle_other 2.341 r_mcangle_it 1.673 r_mcangle_other 1.673 r_angle_refined_deg 1.579 r_scbond_it 1.489 r_scbond_other 1.487 r_mcbond_it 1.128 r_mcbond_other 1.123 r_angle_other_deg 0.994 r_chiral_restr 0.091 r_bond_refined_d 0.012 r_gen_planes_refined 0.008 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 789 Nucleic Acid Atoms Solvent Atoms 98 Heterogen Atoms 2
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling MOLREP phasing