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Crystal structure of Putative succinylglutamate desuccinylase/aspartoacylase (YP_749235.1) from Shewanella frigidimarinA NCIMB 400 at 2.10 A resolution
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 4.5 293 10.0000% Glycerol, 12.5000% polyethylene glycol 300, 0.2000M ammonium sulfate, 0.1M phosphate-citrate pH 4.5, 0.006 M zinc chloride, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 3.01 59.17
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 126.549 α = 90 b = 128.972 β = 90 c = 129.574 γ = 90
Symmetry Space Group F 2 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 2009-11-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL9-2 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 2.1 29.623 99.7 0.106 9.47 30948 -3 31.815
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 2.1 2.17 99.1 0.82 1.7
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 SAD THROUGHOUT 2.1 29.623 30947 1561 99.85 0.162 0.16 0.1816 0.19 0.2045 RANDOM 21.824
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] 2.44 -1.66 -0.78
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.135 r_dihedral_angle_4_deg 14.729 r_dihedral_angle_3_deg 14.053 r_dihedral_angle_1_deg 6.492 r_scangle_it 3.729 r_scbond_it 2.45 r_angle_refined_deg 1.536 r_mcangle_it 1.454 r_angle_other_deg 0.923 r_mcbond_it 0.82
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.135 r_dihedral_angle_4_deg 14.729 r_dihedral_angle_3_deg 14.053 r_dihedral_angle_1_deg 6.492 r_scangle_it 3.729 r_scbond_it 2.45 r_angle_refined_deg 1.536 r_mcangle_it 1.454 r_angle_other_deg 0.923 r_mcbond_it 0.82 r_mcbond_other 0.197 r_chiral_restr 0.097 r_bond_refined_d 0.017 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 2880 Nucleic Acid Atoms Solvent Atoms 200 Heterogen Atoms 18
Software Software Software Name Purpose REFMAC refinement PHENIX refinement SHELX phasing MolProbity model building XSCALE data scaling PDB_EXTRACT data extraction XDS data reduction SHELXD phasing autoSHARP phasing