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Crystal structure of a succinylglutamate desuccinylase (TM1040_2694) from SILICIBACTER SP. TM1040 at 2.00 A resolution
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 277 0.2000M NaCl, 30.0000% PEG-3000, 0.1M TRIS pH 7.0, 0.006 M Calcium Chloride, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.72 54.74
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 99.773 α = 90 b = 99.773 β = 90 c = 137.179 γ = 120
Symmetry Space Group P 63 2 2
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 MARMOSAIC 325 mm CCD Flat collimating mirror, toroid focusing mirror 2010-03-11 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL9-2 0.91837,0.97922,0.97905 SSRL BL9-2
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 2 29.487 99.5 0.157 11.56 27876 -3 28.032
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 2.07 96.6 0.013 1.8
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 MAD THROUGHOUT 2 29.487 27844 1397 99.74 0.163 0.161 0.1664 0.195 0.1962 RANDOM 29.563
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] 0.92 0.46 0.92 -1.38
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.242 r_dihedral_angle_4_deg 24.762 r_dihedral_angle_3_deg 14.023 r_scangle_it 7.279 r_dihedral_angle_1_deg 6.526 r_scbond_it 5.16 r_mcangle_it 2.817 r_mcbond_it 1.724 r_angle_refined_deg 1.513 r_angle_other_deg 0.894
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.242 r_dihedral_angle_4_deg 24.762 r_dihedral_angle_3_deg 14.023 r_scangle_it 7.279 r_dihedral_angle_1_deg 6.526 r_scbond_it 5.16 r_mcangle_it 2.817 r_mcbond_it 1.724 r_angle_refined_deg 1.513 r_angle_other_deg 0.894 r_mcbond_other 0.496 r_chiral_restr 0.094 r_bond_refined_d 0.015 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2493 Nucleic Acid Atoms Solvent Atoms 313 Heterogen Atoms 10
Software Software Software Name Purpose REFMAC refinement PHENIX refinement SOLVE phasing MolProbity model building XSCALE data scaling PDB_EXTRACT data extraction XDS data reduction