☰ Navigation Tabs
Structural and Kinetic Study of an S-Formylglutathione Hydrolase from Agrobacterium tumefaciens
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1PV1 PDB code 1PV1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 293 PEG 3350, MgCl2, Bis-Tris buffer, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.29 46.31
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 68.433 α = 92.41 b = 68.949 β = 99.79 c = 95.648 γ = 98.47
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 IMAGE PLATE RIGAKU RAXIS IV 2006-03-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 1.5418
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 2.01 32.4 95 0.058 23.2 106354 106354
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) 2.02 2.09 80 0.288 4.3 106354
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 PDB code 1PV1 2.01 25 106354 106327 5368 100 0.183 0.183 0.181 0.1807 0.219 0.2191 RANDOM 26.912
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] 0.39 1.32 -0.84 0.7 -0.15 -0.99
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.679 r_dihedral_angle_4_deg 11.911 r_dihedral_angle_3_deg 11.296 r_dihedral_angle_1_deg 5.423 r_scangle_it 2.216 r_scbond_it 1.456 r_angle_refined_deg 1.207 r_mcangle_it 0.927 r_mcbond_it 0.556 r_nbtor_refined 0.301
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.679 r_dihedral_angle_4_deg 11.911 r_dihedral_angle_3_deg 11.296 r_dihedral_angle_1_deg 5.423 r_scangle_it 2.216 r_scbond_it 1.456 r_angle_refined_deg 1.207 r_mcangle_it 0.927 r_mcbond_it 0.556 r_nbtor_refined 0.301 r_nbd_refined 0.184 r_symmetry_vdw_refined 0.173 r_symmetry_hbond_refined 0.124 r_xyhbond_nbd_refined 0.123 r_chiral_restr 0.089 r_metal_ion_refined 0.013 r_bond_refined_d 0.009 r_gen_planes_refined 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 13226 Nucleic Acid Atoms Solvent Atoms 670 Heterogen Atoms 18
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data collection MrBUMP phasing